| Next changeset 1:f3012521ea79 (2015-03-13) |
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Commit message:
Initial commit with version 1.0.0 of the cummeRbund wrapper. |
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added:
cummeRbund.R cummeRbund.xml cummeRbund_macros.xml cummeRbund_options.py test-data/boxplot.png test-data/boxplot.txt test-data/cuffdiff_out.sqlite test-data/dendrogram.png test-data/dendrogram.txt test-data/density.png test-data/density.txt test-data/dispersion.png test-data/dispersion.txt test-data/expressionbarplot.png test-data/expressionbarplot.txt test-data/expressionplot.png test-data/expressionplot.txt test-data/fpkmSCV.png test-data/fpkmSCV.txt test-data/heatmap.png test-data/heatmap.txt test-data/maplot.png test-data/maplot.txt test-data/pca.png test-data/pca.txt test-data/scatter.png test-data/scatter.txt test-data/scatterMatrix.png test-data/scatterMatrix.txt test-data/volcano.png test-data/volcano.txt tool_dependencies.xml |
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| diff -r 000000000000 -r 587c425b4e76 cummeRbund.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cummeRbund.R Tue Dec 23 15:58:27 2014 -0500 |
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| @@ -0,0 +1,146 @@ +## Feature Selection ## +get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) + else if (f == "tss") + return(TSS(myGenes)) + else if (f == "cds") + return(CDS(myGenes)) + else + return(myGenes) +} + +## Main Function ## + +library(argparse) + +parser <- ArgumentParser(description='Create a plot with cummeRbund') + +parser$add_argument('--type', dest='plotType', default='Density', required=TRUE) +parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE) +parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE) +parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE) +parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE) +parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE) +parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE) +parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE) +parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE) +parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE) +parser$add_argument('--border', dest='border', action="store_true", default=FALSE) +parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE) +parser$add_argument('--count', dest='count', action="store_true", default=FALSE) +parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE) +parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE) +parser$add_argument('--features', dest='features', action="store", default="genes") +parser$add_argument('--clustering', dest='clustering', action="store", default="both") +parser$add_argument('--iter_max', dest='iter_max', action="store") +parser$add_argument('--genes', dest='genes', action="append") +parser$add_argument('--k', dest='k', action="store") +parser$add_argument('--x', dest='x', action="store") +parser$add_argument('--y', dest='y', action="store") + +args <- parser$parse_args() + +## Load cummeRbund library +library("cummeRbund") + +## Initialize cuff object +cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE) + +## Print out info +print(cuff) +sink("cuffdb_info.txt") +print(cuff) +print("SAMPLES:") +samples(cuff) +print("REPLICATES:") +replicates(cuff) +print("FEATURES:") +print(annotation(genes(cuff))) +cat(annotation(genes(cuff))[[1]],sep=",") +sink() + +png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png')) +tryCatch({ + if (args$plotType == 'density') { + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10) + } + else if (args$plotType == 'boxplot') { + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10) + } + else if (args$plotType == 'mds') { + MDSplot(genes(cuff), replicates=args$replicates) + } + else if (args$plotType == 'pca') { + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates) + } + else if (args$plotType == 'dendrogram') { + csDendro(genes(cuff), replicates=args$replicates) + } + else if (args$plotType == 'scatter') { + if (args$gene_selector) { + myGenes <- getGenes(cuff, args$genes) + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10) + } + else { + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10) + } + } + else if (args$plotType == 'volcano') { + if (args$gene_selector) { + myGenes <- get_features(getGenes(cuff, args$genes), args$features) + } + else { + myGenes <- genes(cuff) + } + csVolcano(myGenes, args$x, args$y) + } + else if (args$plotType == 'heatmap') { + if (args$gene_selector) { + myGenes <- getGenes(cuff, args$genes) + } + else { + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]]) + } + csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10) + } + else if (args$plotType == 'cluster') { + myGenes <- getGenes(cuff, args$genes) + csCluster(get_features(myGenes, args$features), k=args$k) + } + else if (args$plotType == 'dispersion') { + dispersionPlot(genes(cuff)) + } + else if (args$plotType == 'fpkmSCV') { + fpkmSCVPlot(genes(cuff)) + } + else if (args$plotType == 'scatterMatrix') { + csScatterMatrix(genes(cuff)) + } + else if (args$plotType == 'expressionplot') { + myGenes <- getGenes(cuff, args$genes) + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates) + } + else if (args$plotType == 'expressionbarplot') { + myGeneId <- args$genes + myGenes <- getGenes(cuff, myGeneId) + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates) + } + else if (args$plotType == 'mds') { + MDSplot(genes(cuff),replicates=args$replicates) + } + else if (args$plotType == 'pca') { + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates) + } + else if (args$plotType == 'maplot') { + MAplot(genes(cuff), args$x, args$y, useCount=args$count) + } + else if (args$plotType == 'genetrack') { + myGene <- getGene(cuff, args$genes) + plotTracks(makeGeneRegionTrack(myGene)) + } +},error = function(e) { + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) +}) +devname = dev.off() |
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| diff -r 000000000000 -r 587c425b4e76 cummeRbund.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cummeRbund.xml Tue Dec 23 15:58:27 2014 -0500 |
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| b'@@ -0,0 +1,359 @@\n+<?xml version="1.0"?>\n+<tool id="cummeRbund" name="Plot CuffDiff" version="1.0.0">\n+ <description>data with cummeRbund</description>\n+ <requirements>\n+ <requirement type="set_environment">CUMMERBUND_SCRIPT_PATH</requirement>\n+ <requirement type="package" version="3.1.2">R</requirement>\n+ <requirement type="package" version="2.8.2">cummeRbund</requirement>\n+ </requirements>\n+ <expand macro="stdio" />\n+ <macros>\n+ <import>cummeRbund_macros.xml</import>\n+ </macros>\n+ <code file="cummeRbund_options.py"/>\n+ <command>\n+<![CDATA[\n+#for i, p in enumerate($plots):\n+ R --vanilla --no-save -f \\$CUMMERBUND_SCRIPT_PATH/cummeRbund.R --args\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+ $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10\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+ #end for\n+ #end if\n+ #elif $p.plot.type == "maplot":\n+ --x "$p.plot.x" --y "$p.plot.y" $p.plot.count\n+ #elif $p.plot.type == "volcano":\n+ --x "$p.plot.x" --y "$p.plot.y"\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+ #end for\n+ #end if\n+ #elif $p.plot.type == "heatmap":\n+ --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10\n+ #if len($p.plot.genes) > 0:\n+ #for gene in $p.plot.genes:\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+ #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+ #end if\n+ #if $p.plot.type == "density":\n+ $p.plot.log10\n+ #end if\n+ > "${output}" 2>&1 ;\n+#end for\n+]]></command>\n+ <inputs>\n+ <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />\n+ <repeat name="plots" title="Plots">\n+ <param name="width" type="integer" value="1280" label="The width of the image"/>\n+ <param name="height" type="integer" value="960" label="The height of the image"/>\n+ <conditional name="plot">\n+ <param name="type" type="select" label="Plot type">\n+ <option value="density" selected="true">Density</option>\n+ <option value="boxplot">Boxplot</option>\n+ <option value="mds">MultiDimentional Scaling (MDS) Plot</option>\n+ <option value="pca">Principal Component Analysis (PCA) Plot</option>\n+ <option value="dendrogram">Dendrogram</option>\n+ <option value="scatter">Scatter</option>\n+ <option value="volcano">Volcano</option>\n+ <option value="heatmap">Heatmap</option>\n+ <option value="dispersion">Dispersion</option>\n+ <option value="fpkmSCV">Squared Coefficient of Variation</option>\n+ '..b't>\n+ <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2">\n+ <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />\n+ <repeat name="plots">\n+ <param name="width" value="1280" />\n+ <param name="height" value="960" />\n+ <conditional name="plot">\n+ <param name="type" value="density" />\n+ </conditional>\n+ </repeat>\n+ <output name="output" ftype="txt" file="density.txt" lines_diff="2">\n+ <discovered_dataset designation="density-0" ftype="png" file="density.png" />\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />\n+ <repeat name="plots">\n+ <param name="width" value="1280" />\n+ <param name="height" value="960" />\n+ <conditional name="plot">\n+ <param name="type" value="dendrogram" />\n+ </conditional>\n+ </repeat>\n+ <output name="output" ftype="txt" file="dendrogram.txt" lines_diff="2">\n+ <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />\n+ <repeat name="plots">\n+ <param name="width" value="1280" />\n+ <param name="height" value="960" />\n+ <conditional name="plot">\n+ <param name="type" value="volcano" />\n+ <param name="x" value="q1" />\n+ <param name="y" value="q2" />\n+ </conditional>\n+ </repeat>\n+ <output name="output" ftype="txt" file="volcano.txt" lines_diff="2">\n+ <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />\n+ <repeat name="plots">\n+ <param name="width" value="1280" />\n+ <param name="height" value="960" />\n+ <conditional name="plot">\n+ <param name="type" value="boxplot" />\n+ </conditional>\n+ </repeat>\n+ <output name="output" ftype="txt" file="boxplot.txt" lines_diff="2">\n+ <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />\n+ <repeat name="plots">\n+ <param name="width" value="1280" />\n+ <param name="height" value="960" />\n+ <conditional name="plot">\n+ <param name="type" value="fpkmSCV" />\n+ </conditional>\n+ </repeat>\n+ <output name="output" ftype="txt" file="fpkmSCV.txt" lines_diff="2">\n+ <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.\n+------\n+Based on the `cummeRbund wrapper <http://toolshed.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">doi:10.1038/nprot.2012.016</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 587c425b4e76 cummeRbund_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cummeRbund_macros.xml Tue Dec 23 15:58:27 2014 -0500 |
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| @@ -0,0 +1,47 @@ +<?xml version="1.0"?> +<macros> + <macro name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </macro> + <macro name="replicates_checkbox"> + <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/> + </macro> + <macro name="log10_checkbox"> + <param name="log10" type="boolean" truevalue="--log10" falsevalue="" checked="True" label="Apply log10 transformation on FPKM values?"/> + </macro> + <macro name="xy_selector"> + <param name="x" type="select" label="Sample name for x axis" dynamic_options="get_samples(input_database.dataset.file_name)" /> + <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.dataset.file_name)" /> + </macro> + <macro name="genes_selector"> + <repeat name="genes" title="Genes"> + <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" /> + </repeat> + </macro> + <macro name="features_selector"> + <param name="features" type="select" label="Expression levels to plot?"> + <option value="gene" selected="true">Genes</option> + <option value="isoforms">Isoforms</option> + <option value="tss">TSS</option> + <option value="cds">CDS</option> + </param> + </macro> + <macro name="multiple_genes_conditional"> + <conditional name="multiple_genes"> + <param name="multiple_genes_selector" type="select" label="Limit plot to genes"> + <option value="no" selected="true">Do not limit</option> + <option value="yes">Select genes</option> + </param> + <when value="yes"> + <expand macro="features_selector" /> + <expand macro="genes_selector" /> + </when> + <when value="no" /> + </conditional> + </macro> +</macros> |
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| diff -r 000000000000 -r 587c425b4e76 cummeRbund_options.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cummeRbund_options.py Tue Dec 23 15:58:27 2014 -0500 |
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| @@ -0,0 +1,24 @@ +from galaxy import eggs +eggs.require( 'SQLAlchemy' ) +eggs.require( 'pysqlite>=2' ) +from sqlalchemy import * +from sqlalchemy.sql import and_ +from sqlalchemy import exceptions as sa_exceptions +from sqlalchemy.orm import sessionmaker +from sqlalchemy.orm import scoped_session + +def get_genes( database_path ): + dburi = 'sqlite:///%s' % database_path + engine = create_engine( dburi ) + meta = MetaData( bind=engine ) + db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) ) + gene_ids = db_session.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 ): + dburi = 'sqlite:///%s' % database_path + engine = create_engine( dburi ) + meta = MetaData( bind=engine ) + db_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) ) + samples = db_session.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 000000000000 -r 587c425b4e76 test-data/boxplot.png |
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| Binary file test-data/boxplot.png has changed |
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| diff -r 000000000000 -r 587c425b4e76 test-data/boxplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/boxplot.txt Tue Dec 23 15:58:27 2014 -0500 |
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| b'@@ -0,0 +1,308 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\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$parse_args()\n+> \n+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-boxplot-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmpCu9yWT/tmpPy7OpW/database/files/000/dataset_34.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] FALSE\n+\n+$plotType\n+[1] "boxplot"\n+\n+$replicates\n+[1] TRUE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\n+Loading required package: parallel\n+\n+Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n+\n+The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n+\n+ clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n+ clusterExport, clusterMap, parApply, pa'..b'ase, rebuild = FALSE)\n+> \n+> ## Print out info\n+> print(cuff)\n+CuffSet instance with:\n+\t 2 samples\n+\t 87 genes\n+\t 90 isoforms\n+\t 88 TSS\n+\t 0 CDS\n+\t 87 promoters\n+\t 88 splicing\n+\t 0 relCDS\n+> sink("cuffdb_info.txt")\n+> print(cuff)\n+> print("SAMPLES:")\n+> samples(cuff)\n+> print("REPLICATES:")\n+> replicates(cuff)\n+> print("FEATURES:")\n+> print(annotation(genes(cuff)))\n+> cat(annotation(genes(cuff))[[1]],sep=",")\n+> sink()\n+> \n+> png(filename = args$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$genes)\n++ plotTracks(makeGeneRegionTrack(myGene))\n++ }\n++ },error = function(e) {\n++ write(paste("Failed:", e, sep=" "), stderr())\n++ q("no", 1, TRUE)\n++ })\n+Fontconfig error: Cannot load default config file\n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/dendrogram.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dendrogram.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,309 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\n+> get_features <- function(myGenes, f="gene") {\n++ if (f == "isoforms")\n++ return(isoforms(myGenes))\n++ else if (f == "tss")\n++ return(TSS(myGenes))\n++ else if (f == "cds")\n++ return(CDS(myGenes))\n++ else\n++ return(myGenes)\n++ }\n+> \n+> ## Main Function ##\n+> \n+> library(argparse)\n+Loading required package: proto\n+> \n+> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n+> \n+> parser$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+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-dendrogram-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_43.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] FALSE\n+\n+$plotType\n+[1] "dendrogram"\n+\n+$replicates\n+[1] TRUE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\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, parApp'..b'nstance 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+Fontconfig error: Cannot load default config file\n+\'dendrogram\' with 2 branches and 2 members total, at height 0.7672512 \n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| [ |
| b'@@ -0,0 +1,311 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\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$parse_args()\n+> \n+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-density-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmpqBHFSU/tmpJRwxiS/database/files/001/dataset_1450.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] TRUE\n+\n+$plotType\n+[1] "density"\n+\n+$replicates\n+[1] TRUE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\n+Loading required package: parallel\n+\n+Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n+\n+The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n+\n+ clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n+ clusterExport, clusterMap, parApply, p'..b'promoters\n+\t 88 splicing\n+\t 0 relCDS\n+> sink("cuffdb_info.txt")\n+> print(cuff)\n+> print("SAMPLES:")\n+> samples(cuff)\n+> print("REPLICATES:")\n+> replicates(cuff)\n+> print("FEATURES:")\n+> print(annotation(genes(cuff)))\n+> cat(annotation(genes(cuff))[[1]],sep=",")\n+> sink()\n+> \n+> png(filename = args$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$genes)\n++ plotTracks(makeGeneRegionTrack(myGene))\n++ }\n++ },error = function(e) {\n++ write(paste("Failed:", e, sep=" "), stderr())\n++ q("no", 1, TRUE)\n++ })\n+Fontconfig error: Cannot load default config file\n+Warning messages:\n+1: Removed 65 rows containing non-finite values (stat_density). \n+2: Removed 63 rows containing non-finite values (stat_density). \n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/dispersion.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dispersion.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,308 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\n+> get_features <- function(myGenes, f="gene") {\n++ if (f == "isoforms")\n++ return(isoforms(myGenes))\n++ else if (f == "tss")\n++ return(TSS(myGenes))\n++ else if (f == "cds")\n++ return(CDS(myGenes))\n++ else\n++ return(myGenes)\n++ }\n+> \n+> ## Main Function ##\n+> \n+> library(argparse)\n+Loading required package: proto\n+> \n+> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n+> \n+> parser$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+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-dispersion-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_25.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] FALSE\n+\n+$plotType\n+[1] "dispersion"\n+\n+$replicates\n+[1] FALSE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\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, parAp'..b'ase, 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+Fontconfig error: Cannot load default config file\n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/expressionbarplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expressionbarplot.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,340 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\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$parse_args()\n+> \n+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] TRUE\n+\n+$features\n+[1] "gene"\n+\n+$filename\n+[1] "plot-expressionbarplot-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+[1] "XLOC_000039"\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmpCu9yWT/tmpPy7OpW/database/files/000/dataset_19.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] TRUE\n+\n+$plotType\n+[1] "expressionbarplot"\n+\n+$replicates\n+[1] TRUE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\n+Loading required package: parallel\n+\n+Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n+\n+The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n+\n+ clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n+ clusterEx'..b't(genes(cuff), replicates=args$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\', which will replace the existing scale.\n+ymax not defined: adjusting position using y instead\n+Fontconfig error: Cannot load default config file\n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/expressionplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expressionplot.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,338 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\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$parse_args()\n+> \n+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] TRUE\n+\n+$features\n+[1] "gene"\n+\n+$filename\n+[1] "plot-expressionplot-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+[1] "XLOC_000059"\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmpNZmIuK/tmpbebRiN/database/files/000/dataset_94.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] TRUE\n+\n+$plotType\n+[1] "expressionplot"\n+\n+$replicates\n+[1] TRUE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\n+Loading required package: parallel\n+\n+Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n+\n+The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n+\n+ clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n+ clusterExport, '..b'density\') {\n++ csDensity(genes(cuff), replicates=args$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+Fontconfig error: Cannot load default config file\n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/fpkmSCV.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fpkmSCV.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,313 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\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+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-fpkmSCV-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_49.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] FALSE\n+\n+$plotType\n+[1] "fpkmSCV"\n+\n+$replicates\n+[1] FALSE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\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, p'..b'(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 replace the existing scale.\n+geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use \'method = x\' to change the smoothing method.\n+Fontconfig error: Cannot load default config file\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+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/heatmap.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmap.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,340 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\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$parse_args()\n+> \n+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "gene"\n+\n+$filename\n+[1] "plot-heatmap-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+[1] "XLOC_000078"\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmpCu9yWT/tmpPy7OpW/database/files/000/dataset_22.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] TRUE\n+\n+$labrow\n+[1] TRUE\n+\n+$log10\n+[1] TRUE\n+\n+$plotType\n+[1] "heatmap"\n+\n+$replicates\n+[1] FALSE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\n+Loading required package: parallel\n+\n+Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n+\n+The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n+\n+ clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n+ clusterExport, clusterMap, pa'..b' }\n++ else if (args$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+Fontconfig error: Cannot load default config file\n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/maplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maplot.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,310 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\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+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-maplot-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmpk0xwrM/tmpNNuxXE/database/files/000/dataset_1.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] FALSE\n+\n+$plotType\n+[1] "maplot"\n+\n+$replicates\n+[1] FALSE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+[1] "q1"\n+\n+$y\n+[1] "q2"\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\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, parApp'..b'nce 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+Fontconfig error: Cannot load default config file\n+Warning message:\n+Removed 52 rows containing missing values (geom_point). \n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/pca.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pca.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,308 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\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$parse_args()\n+> \n+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-pca-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmpY6OfpX/tmpXqSg_D/database/files/000/dataset_13.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] FALSE\n+\n+$plotType\n+[1] "pca"\n+\n+$replicates\n+[1] TRUE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\n+Loading required package: parallel\n+\n+Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n+\n+The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n+\n+ clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n+ clusterExport, clusterMap, parApply, parCapply,'..b'ase, rebuild = FALSE)\n+> \n+> ## Print out info\n+> print(cuff)\n+CuffSet instance with:\n+\t 2 samples\n+\t 87 genes\n+\t 90 isoforms\n+\t 88 TSS\n+\t 0 CDS\n+\t 87 promoters\n+\t 88 splicing\n+\t 0 relCDS\n+> sink("cuffdb_info.txt")\n+> print(cuff)\n+> print("SAMPLES:")\n+> samples(cuff)\n+> print("REPLICATES:")\n+> replicates(cuff)\n+> print("FEATURES:")\n+> print(annotation(genes(cuff)))\n+> cat(annotation(genes(cuff))[[1]],sep=",")\n+> sink()\n+> \n+> png(filename = args$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$genes)\n++ plotTracks(makeGeneRegionTrack(myGene))\n++ }\n++ },error = function(e) {\n++ write(paste("Failed:", e, sep=" "), stderr())\n++ q("no", 1, TRUE)\n++ })\n+Fontconfig error: Cannot load default config file\n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/scatter.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scatter.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,308 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\n+> get_features <- function(myGenes, f="gene") {\n++ if (f == "isoforms")\n++ return(isoforms(myGenes))\n++ else if (f == "tss")\n++ return(TSS(myGenes))\n++ else if (f == "cds")\n++ return(CDS(myGenes))\n++ else\n++ return(myGenes)\n++ }\n+> \n+> ## Main Function ##\n+> \n+> library(argparse)\n+Loading required package: proto\n+> \n+> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n+> \n+> parser$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+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-scatter-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmp_cslqP/tmpQijFOJ/database/files/000/dataset_55.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] TRUE\n+\n+$plotType\n+[1] "scatter"\n+\n+$replicates\n+[1] FALSE\n+\n+$smooth\n+[1] TRUE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+[1] "q1"\n+\n+$y\n+[1] "q2"\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\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, parAp'..b'ase, 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+Fontconfig error: Cannot load default config file\n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/scatterMatrix.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scatterMatrix.txt Tue Dec 23 15:58:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,308 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\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$parse_args()\n+> \n+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-scatterMatrix-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_28.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] FALSE\n+\n+$plotType\n+[1] "scatterMatrix"\n+\n+$replicates\n+[1] FALSE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+NULL\n+\n+$y\n+NULL\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\n+Loading required package: parallel\n+\n+Attaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n+\n+The following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n+\n+ clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n+ clusterExport, clusterMap,'..b'ase, rebuild = FALSE)\n+> \n+> ## Print out info\n+> print(cuff)\n+CuffSet instance with:\n+\t 2 samples\n+\t 87 genes\n+\t 90 isoforms\n+\t 88 TSS\n+\t 0 CDS\n+\t 87 promoters\n+\t 88 splicing\n+\t 0 relCDS\n+> sink("cuffdb_info.txt")\n+> print(cuff)\n+> print("SAMPLES:")\n+> samples(cuff)\n+> print("REPLICATES:")\n+> replicates(cuff)\n+> print("FEATURES:")\n+> print(annotation(genes(cuff)))\n+> cat(annotation(genes(cuff))[[1]],sep=",")\n+> sink()\n+> \n+> png(filename = args$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$genes)\n++ plotTracks(makeGeneRegionTrack(myGene))\n++ }\n++ },error = function(e) {\n++ write(paste("Failed:", e, sep=" "), stderr())\n++ q("no", 1, TRUE)\n++ })\n+Fontconfig error: Cannot load default config file\n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
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| diff -r 000000000000 -r 587c425b4e76 test-data/volcano.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/volcano.txt Tue Dec 23 15:58:27 2014 -0500 |
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| b'@@ -0,0 +1,308 @@\n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> ## Feature Selection ##\n+> get_features <- function(myGenes, f="gene") {\n++ if (f == "isoforms")\n++ return(isoforms(myGenes))\n++ else if (f == "tss")\n++ return(TSS(myGenes))\n++ else if (f == "cds")\n++ return(CDS(myGenes))\n++ else\n++ return(myGenes)\n++ }\n+> \n+> ## Main Function ##\n+> \n+> library(argparse)\n+Loading required package: proto\n+> \n+> parser <- ArgumentParser(description=\'Create a plot with cummeRbund\')\n+> \n+> parser$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+> print(args)\n+$border\n+[1] FALSE\n+\n+$clustering\n+[1] "both"\n+\n+$count\n+[1] FALSE\n+\n+$error_bars\n+[1] FALSE\n+\n+$features\n+[1] "genes"\n+\n+$filename\n+[1] "plot-volcano-0.png"\n+\n+$gene_selector\n+[1] FALSE\n+\n+$genes\n+NULL\n+\n+$height\n+[1] 960\n+\n+$input_database\n+[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_46.dat"\n+\n+$iter_max\n+NULL\n+\n+$k\n+NULL\n+\n+$labcol\n+[1] FALSE\n+\n+$labrow\n+[1] FALSE\n+\n+$log10\n+[1] FALSE\n+\n+$plotType\n+[1] "volcano"\n+\n+$replicates\n+[1] FALSE\n+\n+$smooth\n+[1] FALSE\n+\n+$summary\n+[1] FALSE\n+\n+$width\n+[1] 1280\n+\n+$x\n+[1] "q1"\n+\n+$y\n+[1] "q2"\n+\n+> \n+> #q()\n+> \n+> ## Load cummeRbund library\n+> library("cummeRbund")\n+Loading required package: BiocGenerics\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, par'..b'ase, 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+Fontconfig error: Cannot load default config file\n+> devname = dev.off()\n+> \n+> #end for\n+> \n' |
| b |
| diff -r 000000000000 -r 587c425b4e76 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Dec 23 15:58:27 2014 -0500 |
| b |
| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable action="set_to" name="CUMMERBUND_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="cummeRbund" version="2.8.2"> + <repository changeset_revision="5aacc6d160ed" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="3.1.2"> + <repository changeset_revision="7cb487a32bde" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
