| Previous changeset 2:a23d604eb17b (2017-02-28) Next changeset 4:57082662d2e5 (2017-03-17) |
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Commit message:
Uploaded |
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modified:
annoPeakFigure/.Rhistory annoPeakFigure/annoPeakFigure.R annoPeakFigure/annoPeakFigure.xml |
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added:
annoPeakFigure/.Rapp.history annoPeakFigure/tool_dependencies 10.27.23.xml |
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removed:
annoPeakFigure/tool_dependencies.xml |
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| diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/.Rhistory --- a/annoPeakFigure/.Rhistory Tue Feb 28 05:55:29 2017 -0500 +++ b/annoPeakFigure/.Rhistory Fri Mar 17 07:08:49 2017 -0400 |
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| @@ -263,3 +263,4 @@ upsetplot(annotatePeak, vennpie = TRUE) dev.off() getwd() +??GRanges |
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| diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/annoPeakFigure.R --- a/annoPeakFigure/annoPeakFigure.R Tue Feb 28 05:55:29 2017 -0500 +++ b/annoPeakFigure/annoPeakFigure.R Fri Mar 17 07:08:49 2017 -0400 |
| [ |
| @@ -1,9 +1,13 @@ +require("ChIPseeker", quietly = TRUE) +require("ChIPpeakAnno", quietly = TRUE) +require("EnsDb.Hsapiens.v75", quietly = TRUE) + options(warn = -1) +options("download.file.method"="wget") args <- commandArgs(trailingOnly = TRUE) DMR = args[1] -annoPeakFigure1 = args[2] -annoPeakFigure2 = args[3] +annoPeakTable = args[2] #DMR <- ("test-data/DMR.bed") DMRInfo = read.table( @@ -14,28 +18,22 @@ quote = "" ) -DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], - ranges = IRanges - (start = DMRInfo[, 2], end = DMRInfo[, 3])) +peaks <- GRanges(seqnames = DMRInfo[, 1], + ranges = IRanges + (start = DMRInfo[, 2], end = DMRInfo[, 3])) -annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) +annoData <- toGRanges(EnsDb.Hsapiens.v75) +seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) -#annoPeakFigure1 <- ('test-data/annoPeakUpset.png') -#annoPeakFigure2 <- ('test-data/annoPeakAnnoBar.png') +anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite") -png(file = annoPeakFigure1, +#annoPeakFigure <- ('test-data/annoPie.png') + +png(file = annoPeakFigure, width = 1200, height = 600) -plotAnnoBar(annotatePeak) +pie1(table(anno$insideFeature)) dev.off() -png(file = annoPeakFigure2, - width = 1200, - height = 600) - -upsetplot(annotatePeak, vennpie = TRUE) - -dev.off() - |
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| diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/annoPeakFigure.xml --- a/annoPeakFigure/annoPeakFigure.xml Tue Feb 28 05:55:29 2017 -0500 +++ b/annoPeakFigure/annoPeakFigure.xml Fri Mar 17 07:08:49 2017 -0400 |
| [ |
| @@ -1,19 +1,18 @@ <tool id="APfigure" name="annoPeakFigure" version="1.16.2"> <requirements> - <requirement type="package" version="3.2.1">R</requirement> - </requirements> + <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement> +</requirements> <stdio> <exit_code range="1:" /> </stdio> - <command> Rscript $__tool_directory__/annoPeakFigure.R "$DMR" "$annoPeakFigure1" "$annoPeakFigure2"</command> + <command> Rscript $__tool_directory__/annoPeakFigure.R "$DMR" "$annoPeakFigure"</command> <inputs> <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file"> <validator type="empty_field" message="This field is required."/> </param> </inputs> <outputs> - <data format="png" name="annoPeakFigure1" label="annoPeakUpset.png"/> - <data format="png" name="annoPeakFigure2" label="annoPeakAnnoBar.png"/> + <data format="png" name="annoPeakFigure" label="annoPeakFigure.png"/> </outputs> <tests> <test> @@ -24,8 +23,7 @@ </collection> </element> </param> - <output format="png" name="annoPeakFigure" label="test-data/annoPeakUpset.png"/> - <output format="png" name="annoPeakFigure" label="test-data/annoPeakAnnoBar.png"/> + <output format="png" name="annoPeakFigure" label="test-data/annoPeakFigure.png"/> </test> </tests> <help> |
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| diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/tool_dependencies 10.27.23.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annoPeakFigure/tool_dependencies 10.27.23.xml Fri Mar 17 07:08:49 2017 -0400 |
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| b'@@ -0,0 +1,276 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+ <tool_dependency>\n+ <actions>\n+ <action type="setup_r_environment">\n+ <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <package name="R" version="3.2.1" />\n+ </repository>\n+\n+ <package>https://www.bioconductor.org/packages/release/bioc/src/contrib/ChIPseeker_1.10.3.tar.gz</package>\n+ <package>https://www.bioconductor.org/packages/release/bioc/src/contrib/ChIPpeakAnno_3.8.9.tar.gz</package>\n+ <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.26.3.tar.gz</package>\n+ <package>https://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.20.0.tar.gz</package>\n+\n+ <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n+ https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n+ </package>\n+ <package 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| b |
| diff -r a23d604eb17b -r 6bcf1f0bff41 annoPeakFigure/tool_dependencies.xml --- a/annoPeakFigure/tool_dependencies.xml Tue Feb 28 05:55:29 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,279 +0,0 @@\n-<?xml version=\'1.0\' encoding=\'utf-8\'?>\n- <tool_dependency>\n- <actions>\n- <action type="setup_r_environment">\n- <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n- <package name="R" version="3.2.1" />\n- </repository>\n- <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n- https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n- </package>\n- <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n- https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n- </package>\n- <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n- https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n- </package>\n- <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">\n- https://bioarchive.galaxyproject.org/fgsea_1.1.2.tar.gz\n- 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</actions>\n- <readme>\n- </readme>\n- </tool_dependency>\n' |