Mercurial > repos > devteam > draw_stacked_barplots
changeset 0:063ecbe59faf draft
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 10:29:15 -0400 |
| parents | |
| children | e997b710e38a |
| files | draw_stacked_barplots.pl draw_stacked_barplots.xml test-data/categories_criteria.tabular test-data/stacked_barplot.pdf tool_dependencies.xml |
| diffstat | 5 files changed, 2585 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/draw_stacked_barplots.pl Wed Sep 25 10:29:15 2013 -0400 @@ -0,0 +1,78 @@ +#!/usr/bin/perl -w + +# This program draws, in a pdf file, a stacked bars plot for different categories of data and for +# different criteria. For each criterion a stacked bar is drawn, such that the height of each stacked +# sub-bar represents the number of elements in each category satisfying that criterion. +# The input consists of a TABULAR format file, where the left column represents the names of categories +# and the other columns are headed by the names of criteria, such that each data value in the file +# represents the number of elements in a certain category satisfying a certain criterion. +# The output is a PDF file containing a stacked bars plot representing the number of elements in each +# category satisfying each criterion. The drawing is done using R code. + + +use strict; +use warnings; + +my $criterion; +my @criteriaArray = (); +my $criteriaNumber = 0; +my $lineCounter = 0; + +#variable to store the names of R script file +my $r_script; + +# check to make sure having correct files +my $usage = "usage: draw_stacked_bar_plot.pl [TABULAR.in] [PDF.out] \n"; +die $usage unless @ARGV == 2; + +my $categoriesInputFile = $ARGV[0]; + +my $categories_criteria_bars_plot_outputFile = $ARGV[1]; + +#open the input file +open (INPUT, "<", $categoriesInputFile) || die("Could not open file $categoriesInputFile \n"); +open (OUTPUT, ">", $categories_criteria_bars_plot_outputFile) || die("Could not open file $categories_criteria_bars_plot_outputFile \n"); + +# R script to implement the drawing of a stacked bar plot representing thes significant motifs in each category of motifs +#construct an R script file +$r_script = "motif_significance_bar_plot.r"; +open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; +print Rcmd " + #store the table content of the first file into a matrix + categoriesTable <- read.table(\"$categoriesInputFile\", header = TRUE); + categoriesMatrix <- as.matrix(categoriesTable); + + + #compute the sum of elements in the column with the maximum sum in each matrix + columnSumsVector <- colSums(categoriesMatrix); + maxColumn <- max (columnSumsVector); + + if (maxColumn %% 10 != 0){ + maxColumn <- maxColumn + 10; + } + + plotHeight = maxColumn/8; + criteriaVector <- names(categoriesTable); + + pdf(file = \"$categories_criteria_bars_plot_outputFile\", width = length(criteriaVector), height = plotHeight, family = \"Times\", pointsize = 12, onefile = TRUE); + + + + #draw the first barplot + barplot(categoriesMatrix, ylab = \"No. of elements in each category\", xlab = \"Criteria\", ylim = range(0, maxColumn), col = \"black\", density = c(10, 20, 30, 40, 50, 60, 70, 80), angle = c(45, 90, 135), names.arg = criteriaVector); + + #draw the legend + legendX = 0.2; + legendY = maxColumn; + + legend (legendX, legendY, legend = rownames(categoriesMatrix), density = c(10, 20, 30, 40, 50, 60, 70, 80), angle = c(45, 90, 135)); + + dev.off(); + + #eof\n"; +close Rcmd; +system("R --no-restore --no-save --no-readline < $r_script > $r_script.out"); + +#close the input files +close(OUTPUT); +close(INPUT);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/draw_stacked_barplots.xml Wed Sep 25 10:29:15 2013 -0400 @@ -0,0 +1,61 @@ +<tool id="draw_stacked_barplots" name="Draw Stacked Bar Plots" version="1.0.0"> + <description>for different categories and different criteria</description> + <requirements> + <requirement type="package" version="2.11.0">R</requirement> + </requirements> + <command interpreter="perl"> + draw_stacked_barplots.pl $inputFile1 $outputFile1 + </command> + + <inputs> + <param format="tabular" name="inputFile1" type="data" label="Select the input file"/> + </inputs> + + <outputs> + <data format="pdf" name="outputFile1"/> + </outputs> + + <tests> + <test> + <param name="inputFile1" value="categories_criteria.tabular" /> + <output name="outputFile1" file="stacked_barplot.pdf" /> + </test> + </tests> + + <help> + +.. class:: infomark + +**What it does** + +This program draws, in a pdf file, a stacked bars plot for different categories of data and for different criteria. For each criterion a stacked bar is +drawn, such that the height of each stacked sub-bar represents the number of elements in each category satisfying that criterion. + +- The input consists of a TABULAR format file, where the left column represents the names of categories and the other columns are headed by the names of criteria, such that each data value in the file represents the number of elements in a certain category satisfying a certain criterion: + +- The output is a PDF file containing a stacked bars plot representing the number of elements in each category satisfying each criterion. The drawing is done using R code. + +**Example** + +Let us suppose that the input file represent the number of significant motifs in each motif category for each window size:: + + 10bp 20bp 40bp 80bp 160bp 320bp 640bp 1280bp + Deletion_Hotspots 2 3 4 4 5 6 7 7 + Dna_Pol_Pause/Frameshift_Hotspots 8 10 14 17 18 15 19 20 + Indel_Hotspots 1 1 1 2 1 0 0 0 + Insertion_Hotspots 0 0 1 2 2 2 2 5 + Topoisomerase_Cleavage_Sites 2 3 5 4 3 3 4 4 + Translin_Targets 0 0 2 2 3 3 3 2 + VDJ_Recombination_Signals 0 0 1 1 1 2 2 2 + X-like_Sites 4 4 4 5 6 7 7 10 + + +Runnig the program will give the following output:: + + The stacked bars plot representing the data in the input file. + +.. image:: ${static_path}/operation_icons/stacked_bars_plot.png + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/categories_criteria.tabular Wed Sep 25 10:29:15 2013 -0400 @@ -0,0 +1,9 @@ + 10bp 20bp 40bp 80bp 160bp 320bp 640bp 1280bp +Deletion_Hotspots 2 3 4 4 5 6 7 7 +Dna_Pol_Pause/Frameshift_Hotspots 8 10 14 17 18 15 19 20 +Indel_Hotspots 1 1 1 2 1 0 0 0 +Insertion_Hotspots 0 0 1 2 2 2 2 5 +Topoisomerase_Cleavage_Sites 2 3 5 4 3 3 4 4 +Translin_Targets 0 0 2 2 3 3 3 2 +VDJ_Recombination_Signals 0 0 1 1 1 2 2 2 +X-like_Sites 4 4 4 5 6 7 7 10
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390.96 l S +517.48 327.46 m 517.48 390.96 l S +518.38 327.46 m 518.38 390.96 l S +519.28 327.46 m 519.28 390.96 l S +520.18 327.46 m 520.18 390.96 l S +521.08 327.46 m 521.08 390.96 l S +521.98 327.46 m 521.98 390.96 l S +522.88 327.46 m 522.88 390.96 l S +523.78 327.46 m 523.78 390.96 l S +524.68 327.46 m 524.68 390.96 l S +525.58 327.46 m 525.58 390.96 l S +526.48 327.46 m 526.48 390.96 l S +527.38 327.46 m 527.38 390.96 l S +479.79 73.44 m +527.73 73.44 l +527.73 117.89 l +479.79 117.89 l +479.79 73.44 l +S +479.79 117.89 m +527.73 117.89 l +527.73 244.90 l +479.79 244.90 l +479.79 117.89 l +S +479.79 244.90 m +527.73 244.90 l +527.73 244.90 l +479.79 244.90 l +479.79 244.90 l +S +479.79 244.90 m +527.73 244.90 l +527.73 276.65 l +479.79 276.65 l +479.79 244.90 l +S +479.79 276.65 m +527.73 276.65 l +527.73 302.05 l +479.79 302.05 l +479.79 276.65 l +S +479.79 302.05 m +527.73 302.05 l +527.73 314.76 l +479.79 314.76 l +479.79 302.05 l +S +479.79 314.76 m +527.73 314.76 l +527.73 327.46 l +479.79 327.46 l +479.79 314.76 l +S +479.79 327.46 m +527.73 327.46 l +527.73 390.96 l +479.79 390.96 l +479.79 327.46 l +S +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 84.71 47.52 Tm (X10bp) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 142.24 47.52 Tm (X20bp) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 199.77 47.52 Tm (X40bp) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 257.30 47.52 Tm (X80bp) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 311.83 47.52 Tm (X160bp) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 369.37 47.52 Tm (X320bp) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 426.90 47.52 Tm (X640bp) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 481.43 47.52 Tm (X1280bp) Tj +ET +Q q +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 284.07 18.72 Tm (Criteria) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 12.96 153.31 Tm [(No. of elements in each cate) 15 (gory)] TJ +ET +Q q +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +59.04 73.44 m 59.04 390.96 l S +59.04 73.44 m 51.84 73.44 l S +59.04 136.94 m 51.84 136.94 l S +59.04 200.45 m 51.84 200.45 l S +59.04 263.95 m 51.84 263.95 l S +59.04 327.46 m 51.84 327.46 l S +59.04 390.96 m 51.84 390.96 l S +BT +0.000 0.000 0.000 rg +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 70.44 Tm (0) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 130.94 Tm (10) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 194.45 Tm (20) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 257.95 Tm (30) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 321.46 Tm (40) Tj +ET +BT +/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 384.96 Tm (50) Tj +ET +Q q 59.04 73.44 486.72 317.52 re W n +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +77.07 390.96 215.46 -129.60 re S +87.87 378.93 m 89.09 380.16 l S +92.07 372.96 m 96.51 377.39 l S +89.08 358.56 m 89.08 365.76 l S +92.68 358.56 m 92.68 365.76 l S +96.28 358.56 m 96.28 365.76 l S +88.65 344.16 m 87.87 344.95 l S +92.05 344.16 m 87.87 348.34 l S +95.44 344.16 m 88.24 351.36 l S +96.51 346.49 m 91.63 351.36 l S +96.51 349.88 m 95.03 351.36 l S +87.87 335.66 m 89.17 336.96 l S +87.87 333.11 m 91.71 336.96 l S +87.87 330.57 m 94.26 336.96 l S +89.60 329.76 m 96.51 336.66 l S +92.15 329.76 m 96.51 334.12 l S +94.70 329.76 m 96.51 331.57 l S +89.08 315.36 m 89.08 322.56 l S +90.52 315.36 m 90.52 322.56 l S +91.96 315.36 m 91.96 322.56 l S +93.40 315.36 m 93.40 322.56 l S +94.84 315.36 m 94.84 322.56 l S +96.28 315.36 m 96.28 322.56 l S +89.43 300.96 m 87.87 302.52 l S +91.12 300.96 m 87.87 304.22 l S +92.82 300.96 m 87.87 305.91 l S +94.52 300.96 m 87.87 307.61 l S +96.21 300.96 m 89.01 308.16 l S +96.51 302.36 m 90.71 308.16 l S +96.51 304.06 m 92.41 308.16 l S +96.51 305.76 m 94.10 308.16 l S +96.51 307.46 m 95.80 308.16 l S +87.87 293.11 m 88.52 293.76 l S +87.87 291.66 m 89.97 293.76 l S +87.87 290.20 m 91.42 293.76 l S +87.87 288.75 m 92.88 293.76 l S +87.87 287.29 m 94.33 293.76 l S +88.59 286.56 m 95.79 293.76 l S +90.04 286.56 m 96.51 293.02 l S +91.50 286.56 m 96.51 291.57 l S +92.95 286.56 m 96.51 290.11 l S +94.41 286.56 m 96.51 288.66 l S +95.86 286.56 m 96.51 287.21 l S +88.18 272.16 m 88.18 279.36 l S +89.08 272.16 m 89.08 279.36 l S +89.98 272.16 m 89.98 279.36 l S +90.88 272.16 m 90.88 279.36 l S +91.78 272.16 m 91.78 279.36 l S +92.68 272.16 m 92.68 279.36 l S +93.58 272.16 m 93.58 279.36 l S +94.48 272.16 m 94.48 279.36 l S +95.38 272.16 m 95.38 279.36 l S +96.28 272.16 m 96.28 279.36 l S +87.87 380.16 m +96.51 380.16 l +96.51 372.96 l +87.87 372.96 l +87.87 380.16 l +S +87.87 365.76 m +96.51 365.76 l +96.51 358.56 l +87.87 358.56 l +87.87 365.76 l +S +87.87 351.36 m +96.51 351.36 l +96.51 344.16 l +87.87 344.16 l +87.87 351.36 l +S +87.87 336.96 m +96.51 336.96 l +96.51 329.76 l +87.87 329.76 l +87.87 336.96 l +S +87.87 322.56 m +96.51 322.56 l +96.51 315.36 l +87.87 315.36 l +87.87 322.56 l +S +87.87 308.16 m +96.51 308.16 l +96.51 300.96 l +87.87 300.96 l +87.87 308.16 l +S +87.87 293.76 m +96.51 293.76 l +96.51 286.56 l +87.87 286.56 l +87.87 293.76 l +S +87.87 279.36 m +96.51 279.36 l +96.51 272.16 l +87.87 272.16 l +87.87 279.36 l +S +BT +0.000 0.000 0.000 rg +/F2 1 Tf 12.00 0.00 -0.00 12.00 107.31 372.59 Tm (Deletion_Hotspots) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 107.31 358.19 Tm [(Dna_Pol_P) 15 (ause/Frameshift_Hotspots)] TJ +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 107.31 343.79 Tm (Indel_Hotspots) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 107.31 329.39 Tm (Insertion_Hotspots) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 107.31 314.99 Tm [(T) 80 (opoisomerase_Clea) 20 (v) 25 (age_Sites)] TJ +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 107.31 300.59 Tm [(T) 35 (ranslin_T) 80 (ar) 18 (gets)] TJ +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 107.31 286.19 Tm (VDJ_Recombination_Signals) Tj +ET +BT +/F2 1 Tf 12.00 0.00 -0.00 12.00 107.31 271.79 Tm [(X-lik) 10 (e_Sites)] TJ +ET +Q +endstream +endobj +7 0 obj +68908 +endobj +3 0 obj +<< +/Type /Pages +/Kids [ +5 0 R +] +/Count 1 +/MediaBox [0 0 576 450] +>> +endobj +4 0 obj +<< +/ProcSet [/PDF /Text] +/Font <</F2 9 0 R >> +/ExtGState << >> +>> +endobj +8 0 obj +<< +/Type /Encoding +/BaseEncoding /WinAnsiEncoding +/Differences [ 45/minus 96/quoteleft +144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent +/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +>> +endobj +9 0 obj << +/Type /Font +/Subtype /Type1 +/Name /F2 +/BaseFont /Times-Roman +/Encoding 8 0 R +>> endobj +xref +0 10 +0000000000 65535 f +0000000021 00000 n +0000000164 00000 n +0000069275 00000 n +0000069358 00000 n +0000000213 00000 n +0000000293 00000 n +0000069254 00000 n +0000069439 00000 n +0000069696 00000 n +trailer +<< +/Size 10 +/Info 1 0 R +/Root 2 0 R +>> +startxref +69794 +%%EOF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 25 10:29:15 2013 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="2.11.0"> + <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>