| Previous changeset 0:cc2266d3e611 (2017-02-27) |
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Commit message:
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowtext_scatterplot commit 2944aa6b74efcdb8d5cbf31abf27b352dcad9ac9" |
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added:
getDensityPlots_text.R getDensityPlots_text.xml static/images/flowtools/flowtextgraph.png test-data/graph.pdf test-data/graph.png test-data/graph2.png test-data/input.flowtext |
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removed:
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 cc2266d3e611 -r 754d511df1a3 flowtext_scatterplot/getDensityPlots_text.R --- a/flowtext_scatterplot/getDensityPlots_text.R Mon Feb 27 12:58:47 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,153 +0,0 @@ -# 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 cc2266d3e611 -r 754d511df1a3 flowtext_scatterplot/getDensityPlots_text.xml --- a/flowtext_scatterplot/getDensityPlots_text.xml Mon Feb 27 12:58:47 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,76 +0,0 @@ -<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 cc2266d3e611 -r 754d511df1a3 flowtext_scatterplot/static/images/flowtools/flowtextgraph.png |
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| diff -r cc2266d3e611 -r 754d511df1a3 flowtext_scatterplot/test-data/graph.pdf |
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| diff -r cc2266d3e611 -r 754d511df1a3 flowtext_scatterplot/test-data/graph.png |
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| diff -r cc2266d3e611 -r 754d511df1a3 flowtext_scatterplot/test-data/graph2.png |
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| diff -r cc2266d3e611 -r 754d511df1a3 flowtext_scatterplot/test-data/input.flowtext --- a/flowtext_scatterplot/test-data/input.flowtext Mon Feb 27 12:58:47 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b |
| diff -r cc2266d3e611 -r 754d511df1a3 getDensityPlots_text.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getDensityPlots_text.R Tue Jul 14 09:40:13 2020 -0400 |
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| @@ -0,0 +1,158 @@ +#!/usr/bin/env Rscript +# Density Plot Module for Galaxy +# ggplot2 +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Version 1 +# Cristel Thomas +# +# + +library(ggplot2) +library(grid) +library(KernSmooth) +# 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=TRUE, + flag_pdf=FALSE) { + 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) + if (nb_markers == 1) { + warning('There is only one marker selected to plot.') + quit(save = "no", status = 12, runLast = FALSE) + } + 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 + } + } + nb_rows <- ceiling(((nb_markers-1)*nb_markers)/4) + h <- 400 * nb_rows + hp <- 10 * (nb_rows/2) + + if (flag_pdf){ + pdf(output, height=hp, width=10, useDingbats=FALSE, onefile=TRUE) + multiplot(plotlist = plots, cols = 2) + dev.off() + } else { + png(output, type="cairo", width=800, height=h) + multiplot(plotlist = plots, cols = 2) + dev.off() + } +} + +args <- commandArgs(trailingOnly = TRUE) +channels <- list() +flag_default <- FALSE +flag_pdf <- FALSE + +if (args[2]=="None" || args[2]== "" || args[2] == "i.e.:1,3,4") { + flag_default <- TRUE +} else { + channels <- as.numeric(strsplit(args[2], ",")[[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[4] == "PDF"){ + flag_pdf <- TRUE +} +generateGraphFromText(args[1], channels, args[3], flag_default, flag_pdf) |
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| diff -r cc2266d3e611 -r 754d511df1a3 getDensityPlots_text.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getDensityPlots_text.xml Tue Jul 14 09:40:13 2020 -0400 |
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| @@ -0,0 +1,83 @@ +<tool id="gen_density_plots_txt" name="Generate scatter plots" version="1.1+galaxy0" profile="18.01"> + <description>for any given markers in a txt-converted FCS file</description> + <requirements> + <requirement type="package" version="3.3.2">r-ggplot2</requirement> + <requirement type="package" version="2.23_17">r-kernsmooth</requirement> + </requirements> + <stdio> + <exit_code range="1:9" level="fatal" /> + <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" /> + <exit_code range="12" level="fatal" description="Please provide more than one channel to plot" /> + <exit_code range="13:" level="fatal"/> + </stdio> + <command><![CDATA[ + Rscript $__tool_directory__/getDensityPlots_text.R '${input}' '${channels}' '${output}' '${outformat}' + ]]> + </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 Format" help="PDF will be larger files that may take some time to load."> + <option value="PNG">PNG</option> + <option value="PDF">PDF</option> + </param> + </inputs> + <outputs> + <data format="png" name="output" label="Scatter Plots of ${channels} from ${input.name} in ${outformat}"> + <change_format> + <when input="outformat" value="PDF" format="pdf" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input" value="input.flowtext"/> + <param name="channels" value="i.e.:1,3,4"/> + <param name="outformat" value="PDF"/> + <output name="output" file="graph.pdf" compare="sim_size" delta="2000000"/> + </test> + <test> + <param name="input" value="input.flowtext"/> + <param name="channels" value="1,3,5"/> + <param name="outformat" value="PNG"/> + <output name="output" file="graph2.png" compare="sim_size" delta="1000000"/> + </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. + +class:: warningmark + +PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally. + +----- + +**Example** + +*Output*: + +.. image:: ./static/images/flowtools/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 cc2266d3e611 -r 754d511df1a3 test-data/input.flowtext --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.flowtext Tue Jul 14 09:40:13 2020 -0400 |
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|
