| Next changeset 1:413f3e610295 (2020-07-16) |
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fcs_scatterplot/getDensityPlots.R fcs_scatterplot/getDensityPlots.xml fcs_scatterplot/static/images/flowtools/densityplots.png fcs_scatterplot/test-data/graph.pdf fcs_scatterplot/test-data/graph.png fcs_scatterplot/test-data/graph2.png fcs_scatterplot/test-data/testfcs1.fcs |
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| diff -r 000000000000 -r 164cd5384f1d fcs_scatterplot/getDensityPlots.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fcs_scatterplot/getDensityPlots.R Mon Feb 27 12:52:20 2017 -0500 |
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| @@ -0,0 +1,128 @@ +# Density Plot Module for Galaxy +# FlowDensity +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Version 1 +# Cristel Thomas +# +# + +library(flowCore) +library(flowDensity) + +generateGraph <- function(input, channels, output, plot_default, flag_pdf, pdf_out) { + fcs <- read.FCS(input, transformation=F) + ## marker names + markers <- colnames(fcs) + print_markers <- as.vector(pData(parameters(fcs))$desc) + # Update print_markers if the $P?S not in the FCS file + for (i in 1:length(print_markers)) { + if (is.na(print_markers[i])) { + print_markers[i] <- markers[i] + } + } + + if (plot_default) { + channels <- c(grep(colnames(fcs), pattern="Forward scatter", ignore.case=TRUE), + grep(colnames(fcs), pattern="Side scatter", ignore.case=TRUE)) + if (length(channels) == 0){ + channels <- c(grep(colnames(fcs), pattern="FSC"), + grep(colnames(fcs), pattern="SSC")) + if (length(channels) > 2) { + #get first FSC and corresponding SSC + channels <- c(grep(colnames(fcs), pattern="FSC-A"), + grep(colnames(fcs), pattern="SSC-A")) + if (length(channels) == 0) { + channels <- c(grep(colnames(fcs), pattern="FSC-H"), + grep(colnames(fcs), pattern="SSC-H")) + if (length(channels) == 0) { + channels <- c(grep(colnames(fcs), pattern="FSC-W"), + grep(colnames(fcs), pattern="SSC-W")) + } + } + } + } + if (length(channels) == 0) { + warning('No forward/side scatter channels found, no plots will be generated.') + quit(save = "no", status = 10, runLast = FALSE) + } + } + + nb_markers <- length(channels) + for (j in nb_markers) { + if (channels[j] > length(markers)){ + warning('Please indicate markers between 1 and ', length(markers)) + quit(save = "no", status = 10, runLast = FALSE) + } + } + png(output, type="cairo", height=600, width=600) + par(mfrow=c(2,2)) + for (m in 1:(nb_markers - 1)) { + for (n in (m+1):nb_markers) { + plotDens(fcs, c(channels[m],channels[n]), xlab = print_markers[channels[m]], ylab = print_markers[channels[n]]) + } + } + dev.off() + + if (flag_pdf) { + pdf(pdf_out, useDingbats=FALSE, onefile=TRUE) + par(mfrow=c(2,2)) + for (m in 1:(nb_markers - 1)) { + for (n in (m+1):nb_markers) { + plotDens(fcs, c(channels[m],channels[n]), xlab = print_markers[channels[m]], ylab = print_markers[channels[n]]) + } + } + dev.off() + } +} + +checkFCS <- function(input_file, channels, output_file, plot_default, flag_pdf, pdf_out) { + isValid <- F + # Check file beginning matches FCS standard + tryCatch({ + isValid = isFCSfile(input_file) + }, error = function(ex) { + print (paste(" ! Error in isFCSfile", ex)) + }) + + if (isValid) { + generateGraph(input_file, channels, output_file, plot_default, flag_pdf, pdf_out) + } else { + print (paste(input_file, "does not meet FCS standard")) + } +} + +args <- commandArgs(trailingOnly = TRUE) +channels <- "" +flag_default <- FALSE +flag_pdf <- FALSE +pdf_output <- "" + +if (args[3]=="None") { + flag_default <- TRUE +} else { + if (args[3] == "i.e.:1,3,4"){ + flag_default <- TRUE + } else { + channels <- as.numeric(strsplit(args[3], ",")[[1]]) + for (channel in channels){ + if (is.na(channel)){ + quit(save = "no", status = 11, runLast = FALSE) + } + } + if (length(channels) == 1){ + warning('Please indicate more than one marker to plot.') + quit(save = "no", status = 10, runLast = FALSE) + } + } +} + +if (args[5] == "TRUE"){ + pdf_output <- args[6] + flag_pdf <- TRUE +} + +checkFCS(args[2], channels, args[4], flag_default, flag_pdf, pdf_output) |
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| diff -r 000000000000 -r 164cd5384f1d fcs_scatterplot/getDensityPlots.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fcs_scatterplot/getDensityPlots.xml Mon Feb 27 12:52:20 2017 -0500 |
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| @@ -0,0 +1,71 @@ +<tool id="gen_density_plots" name="Generate scatter plots" version="1.0"> + <description>for any given markers in FCS file.</description> + <requirements> + <requirement type="package" version="3.3.0">r</requirement> + <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement> + <requirement type="package" version="1.6.0">bioconductor-flowdensity</requirement> + </requirements> + <stdio> + <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" /> + <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" /> + </stdio> + <command><![CDATA[ + Rscript --slave --vanilla $__tool_directory__/getDensityPlots.R --args "${input}" "${channels}" "${outpng}" $outformat "${outpdf}" + ]]> + </command> + <inputs> + <param format="fcs" name="input" type="data" label="FCS file"/> + <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot FSC vs SSC if the channels are found."/> + <param name="outformat" type="select" label="Output PDF?"> + <option value="FALSE">No, thank you</option> + <option value="TRUE">Yes, please</option> + </param> + </inputs> + <outputs> + <data format="pdf" name="outpdf" label="Scatter Plots of ${channels} from ${input.name}"> + <filter>outformat=="TRUE"</filter> + </data> + <data format="png" name="outpng" label="Scatter Plots of ${channels} from ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="channels" value="1,3"/> + <param name="outformat" value="TRUE"/> + <output name="outpdf" file="graph.pdf" compare="sim_size"/> + <output name="outpng" file="graph.png" compare="sim_size"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="channels" value="i.e.:1,3,4"/> + <param name="outformat" value="FALSE"/> + <output name="outpng" file="graph2.png" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + This tool allows generation of density scatter plots using flowDensity. + +----- + +**Input files** + +This tool takes valid FCS files as input. + +**Output files** + +This tool generates a scatter plot for each marker combination in a single png file. A pdf file can optionally be generated. + +----- + +**Example** + +*Output*: + +.. image:: static/images/densityplots.png + ]]> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu677</citation> + <citation type="doi">10.1186/1471-2105-10-106</citation> + </citations> +</tool> |
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