| Previous changeset 5:78fcfc04fcfe (2017-02-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" |
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modified:
cummeRbund.R cummeRbund.xml cummeRbund_macros.xml cummeRbund_options.py test-data/boxplot.png test-data/dendrogram.png test-data/density.png test-data/dispersion.png test-data/expressionbarplot.png test-data/expressionplot.png test-data/fpkmSCV.png test-data/heatmap.png test-data/maplot.png test-data/pca.png test-data/scatter.png test-data/scatterMatrix.png test-data/volcano.png |
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removed:
test-data/boxplot.txt test-data/dendrogram.txt test-data/density.txt test-data/dispersion.txt test-data/expressionbarplot.txt test-data/expressionplot.txt test-data/fpkmSCV.txt test-data/heatmap.txt test-data/maplot.txt test-data/pca.txt test-data/scatter.txt test-data/scatterMatrix.txt test-data/volcano.txt |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 cummeRbund.R --- a/cummeRbund.R Thu Feb 23 20:24:03 2017 -0500 +++ b/cummeRbund.R Mon Jul 06 20:25:47 2020 -0400 |
| [ |
| b'@@ -1,44 +1,44 @@\n ## Feature Selection ##\n-options(echo=TRUE)\n-get_features <- function(myGenes, f="gene") {\n+options(echo = TRUE)\n+get_features <- function(my_genes, f = "gene") {\n if (f == "isoforms")\n- return(isoforms(myGenes))\n+ return(isoforms(my_genes))\n else if (f == "tss")\n- return(TSS(myGenes))\n+ return(TSS(my_genes))\n else if (f == "cds")\n- return(CDS(myGenes))\n+ return(CDS(my_genes))\n else\n- return(myGenes)\n+ return(my_genes)\n }\n \n ## Main Function ##\n \n library(argparse)\n \n-parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n+parser <- ArgumentParser(description = "Create a plot with cummeRbund")\n \n-parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-parser$add_argument(\'--k\', dest=\'k\', action="store")\n-parser$add_argument(\'--x\', dest=\'x\', action="store")\n-parser$add_argument(\'--y\', dest=\'y\', action="store")\n+parser$add_argument("--type", dest = "plotType", default = "Density", required = TRUE)\n+parser$add_argument("--height", dest = "height", type = "integer", default = 960, required = TRUE)\n+parser$add_argument("--width", dest = "width", type = "integer", default = 1280, required = TRUE)\n+parser$add_argument("--outfile", dest = "filename", default = "plot-unknown-0.png", required = TRUE)\n+parser$add_argument("--input", dest = "input_database", default = "cuffData.db", required = TRUE)\n+parser$add_argument("--smooth", dest = "smooth", action = "store_true", default = FALSE)\n+parser$add_argument("--gene_selector", dest = "gene_selector", action = "store_true", default = FALSE)\n+parser$add_argument("--replicates", dest = "replicates", action = "store_true", default = FALSE)\n+parser$add_argument("--labcol", dest = "labcol", action = "store_true", default = FALSE)\n+parser$add_argument("--labrow", dest = "labrow", action = "store_true", default = FALSE)\n+parser$add_argument("--border", dest = "border", action = "store_true", default = FALSE)\n+parser$add_argument("--summary", dest = "summary", action = "store_true", default = FALSE)\n+parser$add_argument("--count", dest = "count", action = "store_true", default = FALSE)\n+parser$add_argument("--error_bars", dest = "error_bars", action = "store_true", default = FALSE)\n+parser$add_argument("--log10", dest = "log10", action = "store_true", default = FALSE)\n+parser$add_argument("--features", dest = "features", action = "store", default = "gen'..b', args$y)\n- }\n- else if (args$plotType == \'heatmap\') {\n- if (args$gene_selector) {\n- myGenes <- getGenes(cuff, args$genes)\n+ my_genes <- get_features(getGenes(cuff, args$genes), args$features)\n+ } else {\n+ my_genes <- genes(cuff)\n }\n- else {\n- myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n+ csVolcano(my_genes, args$x, args$y)\n+ } else if (args$plotType == "heatmap") {\n+ if (args$gene_selector) {\n+ my_genes <- getGenes(cuff, args$genes)\n+ } else {\n+ my_genes <- getGenes(cuff, annotation(genes(cuff))[[1]])\n }\n- csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n- }\n- else if (args$plotType == \'cluster\') {\n- myGenes <- getGenes(cuff, args$genes)\n- csCluster(get_features(myGenes, args$features), k=args$k)\n- }\n- else if (args$plotType == \'dispersion\') {\n+ csHeatmap(get_features(my_genes, args$features), clustering = args$clustering, labCol = args$labcol, labRow = args$labrow, border = args$border, logMode = args$log10)\n+ } else if (args$plotType == "cluster") {\n+ my_genes <- getGenes(cuff, args$genes)\n+ csCluster(get_features(my_genes, args$features), k = args$k)\n+ } else if (args$plotType == "dispersion") {\n dispersionPlot(genes(cuff))\n- }\n- else if (args$plotType == \'fpkmSCV\') {\n+ } else if (args$plotType == "fpkmSCV") {\n fpkmSCVPlot(genes(cuff))\n- }\n- else if (args$plotType == \'scatterMatrix\') {\n+ } else if (args$plotType == "scatterMatrix") {\n csScatterMatrix(genes(cuff))\n+ } else if (args$plotType == "expressionplot") {\n+ my_genes <- getGenes(cuff, args$genes)\n+ expressionPlot(get_features(my_genes, args$features), drawSummary = args$summary, showErrorbars = args$error_bars, replicates = args$replicates)\n+ } else if (args$plotType == "expressionbarplot") {\n+ my_gene_id <- args$genes\n+ my_genes <- getGenes(cuff, my_gene_id)\n+ expressionBarplot(get_features(my_genes, args$features), showErrorbars = args$error_bars, replicates = args$replicates)\n+ } else if (args$plotType == "mds") {\n+ MDSplot(genes(cuff), replicates = args$replicates)\n+ } else if (args$plotType == "pca") {\n+ PCAplot(genes(cuff), "PC1", "PC2", replicates = args$replicates)\n+ } else if (args$plotType == "maplot") {\n+ MAplot(genes(cuff), args$x, args$y, useCount = args$count)\n+ } else if (args$plotType == "genetrack") {\n+ my_gene <- getGene(cuff, args$genes)\n+ plotTracks(makeGeneRegionTrack(my_gene))\n }\n- else if (args$plotType == \'expressionplot\') {\n- myGenes <- getGenes(cuff, args$genes)\n- expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n- }\n- else if (args$plotType == \'expressionbarplot\') {\n- myGeneId <- args$genes\n- myGenes <- getGenes(cuff, myGeneId)\n- expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n- }\n- else if (args$plotType == \'mds\') {\n- MDSplot(genes(cuff),replicates=args$replicates)\n- }\n- else if (args$plotType == \'pca\') {\n- PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n- }\n- else if (args$plotType == \'maplot\') {\n- MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n- }\n- else if (args$plotType == \'genetrack\') {\n- myGene <- getGene(cuff, args$genes)\n- plotTracks(makeGeneRegionTrack(myGene))\n- }\n-},error = function(e) {\n- write(paste("Failed:", e, sep=" "), stderr())\n+}, error = function(e) {\n+ write(paste("Failed:", e, sep = " "), stderr())\n q("no", 1, TRUE)\n })\n-devname = dev.off()\n+devname <- dev.off()\n+print("cummeRbund finished")\n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 cummeRbund.xml --- a/cummeRbund.xml Thu Feb 23 20:24:03 2017 -0500 +++ b/cummeRbund.xml Mon Jul 06 20:25:47 2020 -0400 |
| [ |
| b'@@ -1,20 +1,22 @@\n <?xml version="1.0"?>\n-<tool id="cummeRbund" name="cummeRbund" version="2.16.0">\n+<tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy1">\n <description>visualize Cuffdiff output</description>\n <macros>\n <import>cummeRbund_macros.xml</import>\n </macros>\n <requirements>\n- <requirement type="package" version="1.0.1">r-argparse</requirement>\n- <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement>\n+ <requirement type="package" version="1">fonts-conda-ecosystem</requirement>\n+ <requirement type="package" version="1.0.4">r-argparse</requirement>\n+ <requirement type="package" version="3.4.1">r-base</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">bioconductor-cummerbund</requirement>\n </requirements>\n <code file="cummeRbund_options.py"/>\n <command detect_errors="aggressive">\n <![CDATA[\n #for i, p in enumerate($plots):\n- Rscript $__tool_directory__/cummeRbund.R\n- --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}"\n- --outfile plot-${p.plot.type}-${i}.png\n+ Rscript --vanilla --slave \'$__tool_directory__/cummeRbund.R\'\n+ --input \'$input_database\' --width $p.width --height $p.height --type "${p.plot.type}"\n+ --outfile \'plot-${p.plot.type}-${i}.png\'\n #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:\n $p.plot.replicates\n #elif $p.plot.type == "scatter":\n@@ -22,7 +24,7 @@\n #if $p.plot.multiple_genes.multiple_genes_selector == "yes":\n --features $p.plot.multiple_genes.features --gene_selector\n #for gene in $p.plot.multiple_genes.genes:\n- --genes ${gene.gene_id}\n+ --genes \'$gene.gene_id\'\n #end for\n #end if\n #elif $p.plot.type == "maplot":\n@@ -32,7 +34,7 @@\n #if $p.plot.multiple_genes.multiple_genes_selector == "yes":\n --features $p.plot.multiple_genes.features --gene_selector\n #for gene in $p.plot.multiple_genes.genes:\n- --genes ${gene.gene_id}\n+ --genes \'$gene.gene_id\'\n #end for\n #end if\n #elif $p.plot.type == "heatmap":\n@@ -40,26 +42,26 @@\n #if len($p.plot.genes) > 0:\n --gene_selector\n #for gene in $p.plot.genes:\n- --genes ${gene.gene_id}\n+ --genes \'$gene.gene_id\'\n #end for\n #end if\n #elif $p.plot.type == "cluster":\n --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max\n #if len($p.plot.genes) > 0:\n #for gene in $p.plot.genes:\n- --genes ${gene.gene_id}\n+ --genes \'$gene.gene_id\'\n #end for\n #end if\n #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:\n #if $p.plot.type == "expressionplot":\n $p.plot.draw_summary\n #end if\n- --features $p.plot.features $p.plot.error_bars --genes ${p.plot.gene_id} $p.plot.replicates $p.plot.log10\n+ --features $p.plot.features $p.plot.error_bars --genes \'$p.plot.gene_id\' $p.plot.replicates $p.plot.log10\n #end if\n #if $p.plot.type == "density":\n $p.plot.log10\n #end if\n- > "${output}" 2>&1 ;\n+ > \'${output}\' 2>&1 ;\n #end for\n ]]></command>\n <inputs>\n@@ -175,7 +177,8 @@\n <param name="y" value="q2" />\n </conditional>\n </repeat>\n- <output name="output" ftype="txt" file="maplot.txt" lines_diff="2">\n+ <output name="output" ftype="txt">\n+ <assert_contents><has_text text="cummeRbund finished" /></assert_contents>\n <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" />\n </output>\n </test>\n@@ -190,7 +193,8 @@\n <param name="y" value="q2" />\n </conditional>\n <'..b' </output>\n </test>\n@@ -244,7 +251,8 @@\n <param name="gene_id" value="XLOC_000059" />\n </conditional>\n </repeat>\n- <output name="output" ftype="txt" file="expressionplot.txt" lines_diff="2">\n+ <output name="output" ftype="txt">\n+ <assert_contents><has_text text="cummeRbund finished" /></assert_contents>\n <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" />\n </output>\n </test>\n@@ -259,7 +267,8 @@\n <param name="gene_id" value="XLOC_000039" />\n </conditional>\n </repeat>\n- <output name="output" ftype="txt" file="expressionbarplot.txt" lines_diff="2">\n+ <output name="output" ftype="txt">\n+ <assert_contents><has_text text="cummeRbund finished" /></assert_contents>\n <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />\n </output>\n </test>\n@@ -278,7 +287,8 @@\n </repeat>\n </conditional>\n </repeat>\n- <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2">\n+ <output name="output" ftype="txt">\n+ <assert_contents><has_text text="cummeRbund finished" /></assert_contents>\n <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />\n </output>\n </test>\n@@ -291,7 +301,8 @@\n <param name="type" value="density" />\n </conditional>\n </repeat>\n- <output name="output" ftype="txt" file="density.txt" lines_diff="2">\n+ <output name="output" ftype="txt">\n+ <assert_contents><has_text text="cummeRbund finished" /></assert_contents>\n <discovered_dataset designation="density-0" ftype="png" file="density.png" />\n </output>\n </test>\n@@ -304,7 +315,8 @@\n <param name="type" value="dendrogram" />\n </conditional>\n </repeat>\n- <output name="output" ftype="txt" file="dendrogram.txt" lines_diff="2">\n+ <output name="output" ftype="txt">\n+ <assert_contents><has_text text="cummeRbund finished" /></assert_contents>\n <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />\n </output>\n </test>\n@@ -319,7 +331,8 @@\n <param name="y" value="q2" />\n </conditional>\n </repeat>\n- <output name="output" ftype="txt" file="volcano.txt" lines_diff="2">\n+ <output name="output" ftype="txt">\n+ <assert_contents><has_text text="cummeRbund finished" /></assert_contents>\n <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />\n </output>\n </test>\n@@ -332,7 +345,8 @@\n <param name="type" value="boxplot" />\n </conditional>\n </repeat>\n- <output name="output" ftype="txt" file="boxplot.txt" lines_diff="2">\n+ <output name="output" ftype="txt">\n+ <assert_contents><has_text text="cummeRbund finished" /></assert_contents>\n <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />\n </output>\n </test>\n@@ -345,7 +359,8 @@\n <param name="type" value="fpkmSCV" />\n </conditional>\n </repeat>\n- <output name="output" ftype="txt" file="fpkmSCV.txt" lines_diff="2">\n+ <output name="output" ftype="txt">\n+ <assert_contents><has_text text="cummeRbund finished" /></assert_contents>\n <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />\n </output>\n </test>\n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 cummeRbund_macros.xml --- a/cummeRbund_macros.xml Thu Feb 23 20:24:03 2017 -0500 +++ b/cummeRbund_macros.xml Mon Jul 06 20:25:47 2020 -0400 |
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| @@ -1,5 +1,6 @@ <?xml version="1.0"?> <macros> + <token name="@TOOL_VERSION@">2.16.0</token> <macro name="replicates_checkbox"> <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/> </macro> |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 cummeRbund_options.py --- a/cummeRbund_options.py Thu Feb 23 20:24:03 2017 -0500 +++ b/cummeRbund_options.py Mon Jul 06 20:25:47 2020 -0400 |
| [ |
| @@ -1,11 +1,13 @@ import sqlite3 -def get_genes( database_path ): - conn = sqlite3.connect( database_path ) - gene_ids = conn.execute( 'SELECT gene_short_name, gene_id FROM genes ORDER BY gene_short_name' ) - return [ ( gene_id[ 0 ], gene_id[ 1 ], False ) for gene_id in gene_ids ] + +def get_genes(database_path): + conn = sqlite3.connect(database_path) + gene_ids = conn.execute('SELECT gene_short_name, gene_id FROM genes ORDER BY gene_short_name') + return [(gene_id[0], gene_id[1], False) for gene_id in gene_ids] -def get_samples( database_path ): - conn = sqlite3.connect( database_path ) - samples = conn.execute( 'SELECT sample_name FROM samples ORDER BY sample_name' ) - return [ ( sample[ 0 ], sample[ 0 ], False ) for sample in samples ] + +def get_samples(database_path): + conn = sqlite3.connect(database_path) + samples = conn.execute('SELECT sample_name FROM samples ORDER BY sample_name') + return [(sample[0], sample[0], False) for sample in samples] |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/boxplot.png |
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| Binary file test-data/boxplot.png has changed |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/boxplot.txt --- a/test-data/boxplot.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,279 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'object\n-> cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)\n-> \n-> ## Print out info\n-> print(cuff)\n-CuffSet instance with:\n-\t 2 samples\n-\t 87 genes\n-\t 90 isoforms\n-\t 88 TSS\n-\t 0 CDS\n-\t 87 promoters\n-\t 88 splicing\n-\t 0 relCDS\n-> sink("cuffdb_info.txt")\n-> print(cuff)\n-> print("SAMPLES:")\n-> samples(cuff)\n-> print("REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-> devname = dev.off()\n-> \n' |
| b |
| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/dendrogram.png |
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| Binary file test-data/dendrogram.png has changed |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/dendrogram.txt --- a/test-data/dendrogram.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,280 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'rebuild = FALSE)\n-> \n-> ## Print out info\n-> print(cuff)\n-CuffSet instance with:\n-\t 2 samples\n-\t 87 genes\n-\t 90 isoforms\n-\t 88 TSS\n-\t 0 CDS\n-\t 87 promoters\n-\t 88 splicing\n-\t 0 relCDS\n-> sink("cuffdb_info.txt")\n-> print(cuff)\n-> print("SAMPLES:")\n-> samples(cuff)\n-> print("REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-\'dendrogram\' with 2 branches and 2 members total, at height 0.7672512 \n-> devname = dev.off()\n-> \n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/density.png |
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| Binary file test-data/density.png has changed |
| b |
| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/density.txt --- a/test-data/density.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,281 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'FALSE)\n-> \n-> ## Print out info\n-> print(cuff)\n-CuffSet instance with:\n-\t 2 samples\n-\t 87 genes\n-\t 90 isoforms\n-\t 88 TSS\n-\t 0 CDS\n-\t 87 promoters\n-\t 88 splicing\n-\t 0 relCDS\n-> sink("cuffdb_info.txt")\n-> print(cuff)\n-> print("SAMPLES:")\n-> samples(cuff)\n-> print("REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-Warning message:\n-Removed 128 rows containing non-finite values (stat_density). \n-> devname = dev.off()\n-> \n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/dispersion.png |
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| Binary file test-data/dispersion.png has changed |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/dispersion.txt --- a/test-data/dispersion.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,282 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b' 2 samples\n-\t 87 genes\n-\t 90 isoforms\n-\t 88 TSS\n-\t 0 CDS\n-\t 87 promoters\n-\t 88 splicing\n-\t 0 relCDS\n-> sink("cuffdb_info.txt")\n-> print(cuff)\n-> print("SAMPLES:")\n-> samples(cuff)\n-> print("REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-Warning messages:\n-1: Transformation introduced infinite values in continuous x-axis \n-2: Transformation introduced infinite values in continuous y-axis \n-> devname = dev.off()\n-> \n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/expressionbarplot.png |
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| Binary file test-data/expressionbarplot.png has changed |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/expressionbarplot.txt --- a/test-data/expressionbarplot.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,311 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'plicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-Getting gene information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting isoforms information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting CDS information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting TSS information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting promoter information:\n-\tdistData\n-Getting splicing information:\n-\tdistData\n-Getting relCDS information:\n-\tdistData\n-Scale for \'colour\' is already present. Adding another scale for \'colour\',\n-which will replace the existing scale.\n-> devname = dev.off()\n-> \n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/expressionplot.png |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/expressionplot.txt --- a/test-data/expressionplot.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,309 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b't, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-Getting gene information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting isoforms information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting CDS information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting TSS information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting promoter information:\n-\tdistData\n-Getting splicing information:\n-\tdistData\n-Getting relCDS information:\n-\tdistData\n-> devname = dev.off()\n-> \n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/fpkmSCV.png |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/fpkmSCV.txt --- a/test-data/fpkmSCV.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,285 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-Scale for \'x\' is already present. Adding another scale for \'x\', which will\n-replace the existing scale.\n-`geom_smooth()` using method = \'loess\'\n-Warning message:\n-In .local(object, FPKMLowerBound, ...) :\n- At least one of your conditions does not have enough replicates to estimate variance. Estimating variance across all conditions instead.\n-> devname = dev.off()\n-> \n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/heatmap.png |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/heatmap.txt --- a/test-data/heatmap.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,311 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'ty(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-Getting gene information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting isoforms information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting CDS information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting TSS information:\n-\tFPKM\n-\tDifferential Expression Data\n-\tAnnotation Data\n-\tReplicate FPKMs\n-\tCounts\n-Getting promoter information:\n-\tdistData\n-Getting splicing information:\n-\tdistData\n-Getting relCDS information:\n-\tdistData\n-Using tracking_id, sample_name as id variables\n-No id variables; using all as measure variables\n-> devname = dev.off()\n-> \n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/maplot.png |
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| Binary file test-data/maplot.png has changed |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/maplot.txt --- a/test-data/maplot.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,281 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'ild = FALSE)\n-> \n-> ## Print out info\n-> print(cuff)\n-CuffSet instance with:\n-\t 2 samples\n-\t 87 genes\n-\t 90 isoforms\n-\t 88 TSS\n-\t 0 CDS\n-\t 87 promoters\n-\t 88 splicing\n-\t 0 relCDS\n-> sink("cuffdb_info.txt")\n-> print(cuff)\n-> print("SAMPLES:")\n-> samples(cuff)\n-> print("REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-Warning message:\n-Removed 52 rows containing missing values (geom_point). \n-> devname = dev.off()\n-> \n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/pca.png |
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| Binary file test-data/pca.png has changed |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/pca.txt --- a/test-data/pca.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,280 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'ile = args$input_database, rebuild = FALSE)\n-> \n-> ## Print out info\n-> print(cuff)\n-CuffSet instance with:\n-\t 2 samples\n-\t 87 genes\n-\t 90 isoforms\n-\t 88 TSS\n-\t 0 CDS\n-\t 87 promoters\n-\t 88 splicing\n-\t 0 relCDS\n-> sink("cuffdb_info.txt")\n-> print(cuff)\n-> print("SAMPLES:")\n-> samples(cuff)\n-> print("REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-Warning: Ignoring unknown aesthetics: label\n-> devname = dev.off()\n-> \n' |
| b |
| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/scatter.png |
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| Binary file test-data/scatter.png has changed |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/scatter.txt --- a/test-data/scatter.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,279 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'object\n-> cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)\n-> \n-> ## Print out info\n-> print(cuff)\n-CuffSet instance with:\n-\t 2 samples\n-\t 87 genes\n-\t 90 isoforms\n-\t 88 TSS\n-\t 0 CDS\n-\t 87 promoters\n-\t 88 splicing\n-\t 0 relCDS\n-> sink("cuffdb_info.txt")\n-> print(cuff)\n-> print("SAMPLES:")\n-> samples(cuff)\n-> print("REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-> devname = dev.off()\n-> \n' |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/scatterMatrix.png |
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| Binary file test-data/scatterMatrix.png has changed |
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| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/scatterMatrix.txt --- a/test-data/scatterMatrix.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,279 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'object\n-> cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)\n-> \n-> ## Print out info\n-> print(cuff)\n-CuffSet instance with:\n-\t 2 samples\n-\t 87 genes\n-\t 90 isoforms\n-\t 88 TSS\n-\t 0 CDS\n-\t 87 promoters\n-\t 88 splicing\n-\t 0 relCDS\n-> sink("cuffdb_info.txt")\n-> print(cuff)\n-> print("SAMPLES:")\n-> samples(cuff)\n-> print("REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-> devname = dev.off()\n-> \n' |
| b |
| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/volcano.png |
| b |
| Binary file test-data/volcano.png has changed |
| b |
| diff -r 78fcfc04fcfe -r c3b54a4b7741 test-data/volcano.txt --- a/test-data/volcano.txt Thu Feb 23 20:24:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,279 +0,0 @@\n-> get_features <- function(myGenes, f="gene") {\n-+ if (f == "isoforms")\n-+ return(isoforms(myGenes))\n-+ else if (f == "tss")\n-+ return(TSS(myGenes))\n-+ else if (f == "cds")\n-+ return(CDS(myGenes))\n-+ else\n-+ return(myGenes)\n-+ }\n-> \n-> ## Main Function ##\n-> \n-> library(argparse)\n-Loading required package: proto\n-> \n-> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n-> \n-> parser$add_argument(\'--type\', dest=\'plotType\', default=\'Density\', required=TRUE)\n-> parser$add_argument(\'--height\', dest=\'height\', type=\'integer\', default=960, required=TRUE)\n-> parser$add_argument(\'--width\', dest=\'width\', type=\'integer\', default=1280, required=TRUE)\n-> parser$add_argument(\'--outfile\', dest=\'filename\', default="plot-unknown-0.png", required=TRUE)\n-> parser$add_argument(\'--input\', dest=\'input_database\', default="cuffData.db", required=TRUE)\n-> parser$add_argument(\'--smooth\', dest=\'smooth\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--gene_selector\', dest=\'gene_selector\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--replicates\', dest=\'replicates\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labcol\', dest=\'labcol\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--labrow\', dest=\'labrow\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--border\', dest=\'border\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--summary\', dest=\'summary\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--count\', dest=\'count\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--error_bars\', dest=\'error_bars\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--log10\', dest=\'log10\', action="store_true", default=FALSE)\n-> parser$add_argument(\'--features\', dest=\'features\', action="store", default="genes")\n-> parser$add_argument(\'--clustering\', dest=\'clustering\', action="store", default="both")\n-> parser$add_argument(\'--iter_max\', dest=\'iter_max\', action="store")\n-> parser$add_argument(\'--genes\', dest=\'genes\', action="append")\n-> parser$add_argument(\'--k\', dest=\'k\', action="store")\n-> parser$add_argument(\'--x\', dest=\'x\', action="store")\n-> parser$add_argument(\'--y\', dest=\'y\', action="store")\n-> \n-> args <- parser$parse_args()\n-> \n-> ## Load cummeRbund library\n-> library("cummeRbund")\n-Loading required package: BiocGenerics\n-Loading required package: methods\n-Loading required package: parallel\n-\n-Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n-\n- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n- clusterExport, clusterMap, parApply, parCapply, parLapply,\n- parLapplyLB, parRapply, parSapply, parSapplyLB\n-\n-The following objects are masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- IQR, mad, xtabs\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- anyDuplicated, append, as.data.frame, cbind, colnames, do.call,\n- duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,\n- is.unsorted, lapply, lengths, Map, mapply, match, mget, order,\n- paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,\n- Reduce, rownames, sapply, setdiff, sort, table, tapply, union,\n- unique, unsplit, which, which.max, which.min\n-\n-Loading required package: RSQLite\n-Loading required package: DBI\n-Loading required package: ggplot2\n-Loading required package: reshape2\n-Loading required package: fastcluster\n-\n-Attaching package: \xe2\x80\x98fastcluster\xe2\x80\x99\n-\n-The following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n-\n- hclust\n-\n-Loading required package: rtracklayer\n-Loading required package: GenomicRanges\n-Loading required package: stats4\n-Loading required package: S4Vectors\n-\n-Attaching package: \xe2\x80\x98S4Vectors\xe2\x80\x99\n-\n-The following objects are masked from \xe2\x80\x98package:base\xe2\x80\x99:\n-\n- colMeans, colSums, expand.grid, rowMeans, rowSums\n-\n-Loading required package: IRanges\n-Loading required package: Genome'..b'object\n-> cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)\n-> \n-> ## Print out info\n-> print(cuff)\n-CuffSet instance with:\n-\t 2 samples\n-\t 87 genes\n-\t 90 isoforms\n-\t 88 TSS\n-\t 0 CDS\n-\t 87 promoters\n-\t 88 splicing\n-\t 0 relCDS\n-> sink("cuffdb_info.txt")\n-> print(cuff)\n-> print("SAMPLES:")\n-> samples(cuff)\n-> print("REPLICATES:")\n-> replicates(cuff)\n-> print("FEATURES:")\n-> print(annotation(genes(cuff)))\n-> cat(annotation(genes(cuff))[[1]],sep=",")\n-> sink()\n-> \n-> png(filename = args$filename, width = args$width, height = args$height, type=c(\'cairo-png\'))\n-> tryCatch({\n-+ if (args$plotType == \'density\') {\n-+ csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'boxplot\') {\n-+ csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'dendrogram\') {\n-+ csDendro(genes(cuff), replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'scatter\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ else {\n-+ csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)\n-+ }\n-+ }\n-+ else if (args$plotType == \'volcano\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- get_features(getGenes(cuff, args$genes), args$features)\n-+ }\n-+ else {\n-+ myGenes <- genes(cuff)\n-+ }\n-+ csVolcano(myGenes, args$x, args$y)\n-+ }\n-+ else if (args$plotType == \'heatmap\') {\n-+ if (args$gene_selector) {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ }\n-+ else {\n-+ myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])\n-+ }\n-+ csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)\n-+ }\n-+ else if (args$plotType == \'cluster\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ csCluster(get_features(myGenes, args$features), k=args$k)\n-+ }\n-+ else if (args$plotType == \'dispersion\') {\n-+ dispersionPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'fpkmSCV\') {\n-+ fpkmSCVPlot(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'scatterMatrix\') {\n-+ csScatterMatrix(genes(cuff))\n-+ }\n-+ else if (args$plotType == \'expressionplot\') {\n-+ myGenes <- getGenes(cuff, args$genes)\n-+ expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'expressionbarplot\') {\n-+ myGeneId <- args$genes\n-+ myGenes <- getGenes(cuff, myGeneId)\n-+ expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'mds\') {\n-+ MDSplot(genes(cuff),replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'pca\') {\n-+ PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)\n-+ }\n-+ else if (args$plotType == \'maplot\') {\n-+ MAplot(genes(cuff), args$x, args$y, useCount=args$count)\n-+ }\n-+ else if (args$plotType == \'genetrack\') {\n-+ myGene <- getGene(cuff, args$genes)\n-+ plotTracks(makeGeneRegionTrack(myGene))\n-+ }\n-+ },error = function(e) {\n-+ write(paste("Failed:", e, sep=" "), stderr())\n-+ q("no", 1, TRUE)\n-+ })\n-> devname = dev.off()\n-> \n' |
