Mercurial > repos > iuc > volcanoplot

annotate test-data/out.rscript @ 5:44608d0193ed draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
author iuc
date Sun, 06 Jun 2021 09:12:22 +0000
parents
children 83c573f2e73c
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44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
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44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
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2 # Galaxy settings start ---------------------------------------------------
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4 # setup R error handling to go to stderr
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5 options(show.error.messages = F, error = function() {cat(geterrmessage(), file = stderr()); q("no", 1, F)})
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7 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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11 # Load packages -----------------------------------------------------------
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13 suppressPackageStartupMessages({
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14 library(dplyr)
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15 library(ggplot2)
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16 library(ggrepel)
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17 })
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20 # Import data ------------------------------------------------------------
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22 # Check if header is present by checking if P value column is numeric or not
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24 first_line <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpfpemuuun/files/8/3/7/dataset_8374ef6b-02c7-46f1-afc9-408a2a6cbde4.dat', header = FALSE, nrow = 1)
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26 first_pvalue <- first_line[, 3]
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28 if (is.numeric(first_pvalue)) {
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29 print("No header row detected")
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30 results <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpfpemuuun/files/8/3/7/dataset_8374ef6b-02c7-46f1-afc9-408a2a6cbde4.dat', header = FALSE)
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31 } else {
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32 print("Header row detected")
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33 results <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpfpemuuun/files/8/3/7/dataset_8374ef6b-02c7-46f1-afc9-408a2a6cbde4.dat', header = TRUE)
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34 }
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37 # Format data ------------------------------------------------------------
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38
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39 # Create columns from the column numbers specified
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40 results <- results %>% mutate(fdr = .[[4]],
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41 pvalue = .[[3]],
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42 logfc = .[[2]],
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43 labels = .[[1]])
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44
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45 # Get names for legend
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46 down <- unlist(strsplit('Down,Not Sig,Up', split = ","))[1]
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47 notsig <- unlist(strsplit('Down,Not Sig,Up', split = ","))[2]
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48 up <- unlist(strsplit('Down,Not Sig,Up', split = ","))[3]
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49
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50 # Set colours
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51 colours <- setNames(c("cornflowerblue", "grey", "firebrick"), c(down, notsig, up))
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52
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53 # Create significant (sig) column
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54 results <- mutate(results, sig = case_when(
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55 fdr < 0.05 & logfc > 0.0 ~ up,
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56 fdr < 0.05 & logfc < -0.0 ~ down,
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57 TRUE ~ notsig))
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60 # Specify genes to label --------------------------------------------------
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61 labelfile <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpfpemuuun/files/4/2/f/dataset_42fc8a63-f9cc-435b-9bb3-dd106b708cd9.dat')
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62 results <- mutate(results, labels = ifelse(labels %in% labelfile[, 1], labels, ""))
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64
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65 # Create plot -------------------------------------------------------------
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67 pdf("out.pdf")
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68 p <- ggplot(results, aes(x = logfc, y = -log10(pvalue))) +
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69 geom_point(aes(colour = sig)) +
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70 scale_color_manual(values = colours) +
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71 scale_fill_manual(values = colours) +
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72 theme(panel.grid.major = element_blank(),
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73 panel.grid.minor = element_blank(),
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74 panel.background = element_blank(),
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75 axis.line = element_line(colour = "black"),
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76 legend.key = element_blank())
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82
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83 # Set legend title
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84 p <- p + labs(colour = "")
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85
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86 # Add gene labels in boxes
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87 p <- p + geom_label_repel(aes(label = labels, fill = sig),
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88 segment.colour = "black",
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89 colour = "white",
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90 min.segment.length = 0,
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91 show.legend = FALSE)
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92
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93 print(p)
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94 dev.off()
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95
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96
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97 # Save RData -------------------------------------------------------------
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98 save.image(file="volcanoplot.RData")
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99
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100
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101 # R and Package versions -------------------------------------------------
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102 sessionInfo()
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103