Mercurial > repos > iuc > volcanoplot
annotate volcanoplot.R @ 0:59ebf2c42c0e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
author | iuc |
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date | Tue, 23 Oct 2018 06:57:26 -0400 |
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children | 7b7303fa20e3 |
rev | line source |
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0
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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1 # setup R error handling to go to stderr |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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3 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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4 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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5 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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6 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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7 suppressPackageStartupMessages({ |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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8 library(dplyr) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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9 library(getopt) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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10 library(ggplot2) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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11 library(ggrepel) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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12 }) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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13 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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14 options(stringAsFactors = FALSE, useFancyQuotes = FALSE) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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15 args <- commandArgs(trailingOnly = TRUE) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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16 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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17 spec <- matrix(c( |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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18 "input", "i", 1, "character", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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19 "fdr_col", "a", 1, "integer", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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20 "pval_col", "p", 1, "integer", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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21 "lfc_col", "c", 1, "integer", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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22 "label_col", "l", 1, "integer", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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23 "signif_thresh", "s", 1, "double", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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24 "lfc_thresh", "x", 1, "double", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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25 "label_file", "f", 1, "character", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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26 "top_num", "t", 1, "integer", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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27 "title", "T", 1, "character", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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28 "xlab", "X", 1, "character", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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29 "ylab", "Y", 1, "character", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
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30 "legend", "L", 1, "character", |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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31 "llabs", "z", 1, "character"), |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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32 byrow=TRUE, ncol=4) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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33 opt <- getopt(spec) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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34 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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35 # Below modified from http://www.gettinggeneticsdone.com/2016/01/repel-overlapping-text-labels-in-ggplot2.html |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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36 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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37 results <- read.delim(opt$input) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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38 results$fdr <- results[, opt$fdr_col] |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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39 results$Pvalue <- results[, opt$pval_col] |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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40 results$logFC <- results[, opt$lfc_col] |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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41 results$labels <- results[, opt$label_col] |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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42 label_down <- unlist(strsplit(opt$llabs, split=","))[1] |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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43 label_notsig <- unlist(strsplit(opt$llabs, split=","))[2] |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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44 label_up <- unlist(strsplit(opt$llabs, split=","))[3] |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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45 colours <- setNames(c("cornflowerblue","grey","firebrick"),c(label_down,label_notsig,label_up)) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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46 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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47 results <- mutate(results, sig=ifelse((fdr<opt$signif_thresh & logFC>opt$lfc_thresh), label_up, ifelse((fdr<opt$signif_thresh & logFC < -opt$lfc_thresh),label_down, label_notsig))) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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48 results <- results[order(results$Pvalue),] |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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49 if (!is.null(opt$label_file)) { |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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50 labelfile <- read.delim(opt$label_file) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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51 tolabel <- filter(results, labels %in% labelfile[, 1]) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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52 } else if (!is.null(opt$top_num)) { |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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53 tolabel <- filter(results, fdr<opt$signif_thresh) %>% top_n(opt$top_num) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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54 } else { |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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55 tolabel <- filter(results, fdr<opt$signif_thresh) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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56 } |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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57 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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58 pdf("out.pdf") |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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59 p <- ggplot(results, aes(logFC, -log10(Pvalue))) + |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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60 geom_point(aes(col=sig)) + |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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61 geom_label_repel(data=tolabel, aes(label=labels, fill=factor(sig)), colour="white", segment.colour="black", show.legend=FALSE) + |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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62 scale_color_manual(values=colours) + |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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63 scale_fill_manual(values=colours) + |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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64 theme(panel.grid.major = element_blank(), |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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65 panel.grid.minor = element_blank(), |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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66 panel.background = element_blank(), |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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67 axis.line = element_line(colour = "black"), |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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68 legend.key=element_blank()) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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69 if (!is.null(opt$title)) { |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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70 p <- p + ggtitle(opt$title) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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71 } |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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72 if (!is.null(opt$xlab)) { |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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73 p <- p + xlab(opt$xlab) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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74 } |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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75 if (!is.null(opt$ylab)) { |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
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76 p <- p + ylab(opt$ylab) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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77 } |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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78 if (!is.null(opt$legend)) { |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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79 p <- p + labs(colour=opt$legend) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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80 } else { |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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81 p <- p + labs(colour="") |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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82 } |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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83 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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84 print(p) |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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85 dev.off() |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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86 |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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87 cat("Session information:\n\n") |
59ebf2c42c0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
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88 sessionInfo() |