Mercurial > repos > iuc > gwastools_manhattan_plot
changeset 0:c4bf5e913c2e draft default tip
"planemo upload commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
| author | iuc |
|---|---|
| date | Fri, 11 Oct 2019 17:31:09 -0400 |
| parents | |
| children | |
| files | manhattan.R manhattan_plot.xml test-data/sampledata.tsv test-data/testgraph.pdf |
| diffstat | 4 files changed, 161 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/manhattan.R Fri Oct 11 17:31:09 2019 -0400 @@ -0,0 +1,60 @@ +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +suppressPackageStartupMessages({ + library(GWASTools) + library(optparse) +}) +option_list <- list( + make_option(c("-f", "--file"), type="character", help="RInput GWAS file"), + make_option("--pval", type="integer", help="Pvalue column"), + make_option("--chromosome", type="integer", help="Chromosome column"), + make_option("--ymin", type="double", help="Min y value"), + make_option("--ymax", type="double", help="Max y value"), + make_option("--trunc", help="Show truncation lines", action="store_true"), + make_option("--sig", type="double", help="Significance level for lines"), + make_option("--thin", type="double", help="Thinning value", action="store_true", dest="thin"), + make_option("--ppb", type="integer", help="Points per bin, if thinning value is specified", action="store_true")) +args <- parse_args(OptionParser(option_list=option_list)) +file <- args$file +data <- read.table(args$file, header=TRUE) +pval <- data[,args$pval] +chromosome <- data[,args$chromosome] +if(!is.null(args$ymin) & !is.null(args$ymax)){ + ylimit <- c(args$ymin,args$ymax) +}else if(xor(!is.null(args$ymin), !is.null(args$ymax))){ + print("If specifying range, both ymin and ymax must be set") + ylimit <- NULL +}else{ + ylimit <- NULL +} +if(is.null(args$trunc)){ + trunc <- FALSE +}else{ + trunc <- TRUE +} +if(!is.null(args$sig)){ + sig <- args$sig +}else{ + sig <- NULL +} +if(!is.null(args$thin)){ + thin = args$thin + if(thin == 0){ + thin = NULL + } +}else{ + thin <- FALSE +} +if(!is.null(thin) & !is.null(args$ppb)){ + ppb = args$ppb +} +pdf("manhattan.pdf") +if(isFALSE(thin)){ + manhattanPlot(pval, chromosome, ylim=ylimit, trunc.lines=trunc, signif=sig) +}else{ + manhattanPlot(pval, chromosome, ylim=ylimit, trunc.lines=trunc, signif=sig, thinThreshold = thin, pointsPerBin = ppb) +} +invisible(dev.off())
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/manhattan_plot.xml Fri Oct 11 17:31:09 2019 -0400 @@ -0,0 +1,88 @@ +<tool id="gwastools_manhattan_plot" name="Manhattan plot" version="0.1.0" python_template_version="3.5"> + <description>Generate plots for use with GWAS pipelines</description> + <requirements> + <requirement type="package" version="3.6">r-base</requirement> + <requirement type="package" version="1.30.0">bioconductor-gwastools</requirement> + <requirement type="package" version="1.6.4">r-optparse</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/manhattan.R' + --file '${file}' + --pval ${pvals} + --chromosome ${chromosome} + #if $ymax: + --ymax ${ymax} + #end if + #if $ymin: + --ymin ${ymin} + #end if + ${trunc} + #if $sig: + --sig ${sig} + #end if + #if $thinselect.thinning == 'Yes': + --thin ${thinselect.thin} + #if $thinselect.ppb: + --ppb ${thinselect.ppb} + #end if + #end if + ]]></command> + <inputs> + <param name="file" type="data" format="tsv,tabular" label="GWAS data file"/> + <param name="chromosome" type="data_column" data_ref="file" label="Chromosome column number"/> + <param name="pvals" type="data_column" data_ref="file" label="P-values column number"/> + <param name="ymax" type = "float" optional="true" label="Y max"/> + <param name="ymin" type = "float" optional="true" label="Y min"/> + <param name="trunc" type="boolean" truevalue="--trunc" falsevalue="" label="Show truncation lines?"/> + <param name="sig" type="float" optional="true" label="Genome-wide significance level for plotting horizontal line." help="If not specified, no line will be drawn."/> + <conditional name="thinselect"> + <param name="thinning" type="select" label='Specify thinning value?'> + <option value="Yes"/> + <option value="No"/> + </param> + <when value="Yes"> + <param name="thin" type="float" value="0" label="Threshold for thinning points" help="If not specified, value is -log10(val)"/> + <param name="ppb" type="integer" optional="true" label="Points per bin"/> + </when> + <when value="No"/> + </conditional> + </inputs> + <outputs> + <data name="manhattanout" format="pdf" from_work_dir="manhattan.pdf" label="Manhattan plot on ${on_string}"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="file" value="sampledata.tsv"/> + <param name="chromosome" value="2"/> + <param name="pvals" value="4"/> + <param name="ymin" value="0.2"/> + <param name="trunc" value="--trunc"/> + <param name="ymax" value="2"/> + <param name="sig" value="0.05"/> + <conditional name="thinselect"> + <param name="thinning" value="yes"/> + <param name="thin" value="1"/> + <param name="ppb" value="1"/> + </conditional> + <output name="manhattanout" ftype="pdf" value="testgraph.pdf" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + Generates a manhattan plot for GWAS data + + Input data format example: + + SNP CHR Pos P + rs1 1 1 0.9148 + rs2 1 2 0.9371 + rs3 1 3 0.2861 + rs4 1 4 0.8304 + rs5 1 5 0.6417 + rs6 1 6 0.5191 + rs16468 22 533 0.1779 + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts610</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampledata.tsv Fri Oct 11 17:31:09 2019 -0400 @@ -0,0 +1,13 @@ +SNP CHR Pos P +rs1 1 1 0.9148 +rs2 1 2 0.9371 +rs3 1 3 0.2861 +rs4 1 4 0.8304 +rs5 1 5 0.6417 +rs6 1 6 0.5191 +rs16465 22 530 0.5644 +rs16466 22 531 0.1383 +rs16467 22 532 0.3937 +rs16468 22 533 0.1779 +rs16469 22 534 0.2393 +rs16470 22 535 0.2630