| Next changeset 1:754d511df1a3 (2020-07-14) |
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flowtext_scatterplot/getDensityPlots_text.R flowtext_scatterplot/getDensityPlots_text.xml flowtext_scatterplot/static/images/flowtools/flowtextgraph.png flowtext_scatterplot/test-data/graph.pdf flowtext_scatterplot/test-data/graph.png flowtext_scatterplot/test-data/graph2.png flowtext_scatterplot/test-data/input.flowtext |
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| diff -r 000000000000 -r cc2266d3e611 flowtext_scatterplot/getDensityPlots_text.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowtext_scatterplot/getDensityPlots_text.R Mon Feb 27 12:58:47 2017 -0500 |
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| @@ -0,0 +1,153 @@ +# Density Plot Module for Galaxy +# ggplot2 +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Version 1 +# Cristel Thomas +# +# + +library(ggplot2) +library(grid) +# Multiple plot function +# from http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_%28ggplot2%29/ +# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects) +# - cols: Number of columns in layout +# - layout: A matrix specifying the layout. If present, 'cols' is ignored. +# +# If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE), +# then plot 1 will go in the upper left, 2 will go in the upper right, and +# 3 will go all the way across the bottom. +# +multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) { + # Make a list from the ... arguments and plotlist + plots <- c(list(...), plotlist) + numPlots = length(plots) + + # If layout is NULL, then use 'cols' to determine layout + if (is.null(layout)) { + # Make the panel + # ncol: Number of columns of plots + # nrow: Number of rows needed, calculated from # of cols + layout <- matrix(seq(1, cols * ceiling(numPlots/cols)), + ncol = cols, nrow = ceiling(numPlots/cols)) + } + + if (numPlots==1) { + print(plots[[1]]) + } else { + # Set up the page + grid.newpage() + pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout)))) + + # Make each plot, in the correct location + for (i in 1:numPlots) { + # Get the i,j matrix positions of the regions that contain this subplot + matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE)) + print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row, + layout.pos.col = matchidx$col)) + } + } +} + +generateGraphFromText <- function(input, channels, output, plot_default, flag_pdf, pdf_out) { + fcs <- read.table(input, header = TRUE, sep = "\t", check.names = FALSE) + ## marker names + markers <- colnames(fcs) + + 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) + } + } + + plots <- list() + i <- 0 + for (m in 1:(nb_markers - 1)) { + for (n in (m+1):nb_markers) { + x <- fcs[,channels[m]] + y <- fcs[,channels[n]] + df <- data.frame(x = x, y = y, + d = densCols(x, y, colramp = colorRampPalette(rev(rainbow(10, end = 4/6))))) + p <- ggplot(df) + + geom_point(aes(x, y, col = d), size = 0.2) + + scale_color_identity() + + theme_bw() + + labs(x = markers[channels[m]]) + + labs(y = markers[channels[n]]) + i <- i + 1 + plots[[i]] <- p + } + } + png(output, type="cairo", width=800, height=800) + multiplot(plotlist = plots, cols = 2) + dev.off() + if (flag_pdf){ + pdf(pdf_out, useDingbats=FALSE, onefile=TRUE) + multiplot(plotlist = plots, cols = 2) + dev.off() + } +} + +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 +} +generateGraphFromText(args[2], channels, args[4], flag_default, flag_pdf, pdf_output) |
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| diff -r 000000000000 -r cc2266d3e611 flowtext_scatterplot/getDensityPlots_text.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowtext_scatterplot/getDensityPlots_text.xml Mon Feb 27 12:58:47 2017 -0500 |
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| @@ -0,0 +1,76 @@ +<tool id="gen_density_plots_txt" name="Generate scatter plots" version="1.0"> + <description>for any given markers in a txt-converted FCS file.</description> + <requirements> + <requirement type="package" version="3.3.0">r</requirement> + <requirement type="package" version="2.1.0">r-ggplot2</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 $__tool_directory__/getDensityPlots_text.R --args "${input}" "${channels}" "${outpng}" $outformat "${outpdf}" + ]]> + </command> + <inputs> + <param format="flowtext" name="input" type="data" label="txt-converted 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="PDF 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="input.flowtext"/> + <param name="channels" value="i.e.:1,3,4"/> + <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="input.flowtext"/> + <param name="channels" value="1,3,5"/> + <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 ggplot2. + +----- + +**Input files** + +This tool takes txt-converted 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/flowtextgraph.png + ]]> + </help> + <citations> + <citation type="bibtex">@BOOK{, + author = {Hadley Wickham}, + title = {ggplot2: Elegant Graphics for Data Analysis}, + publisher = {Springer-Verlag New York}, + year = {2009}, + isbn = {978-0-387-98140-6}, + url = {http://ggplot2.org}, + }</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r cc2266d3e611 flowtext_scatterplot/static/images/flowtools/flowtextgraph.png |
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| diff -r 000000000000 -r cc2266d3e611 flowtext_scatterplot/test-data/input.flowtext --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowtext_scatterplot/test-data/input.flowtext Mon Feb 27 12:58:47 2017 -0500 |
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|
