Mercurial > repos > iuc > volcanoplot

comparison 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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4:73b8cb5bddcd 5:44608d0193ed
1
2 # Galaxy settings start ---------------------------------------------------
3
4 # setup R error handling to go to stderr
5 options(show.error.messages = F, error = function() {cat(geterrmessage(), file = stderr()); q("no", 1, F)})
6
7 # we need that to not crash galaxy with an UTF8 error on German LC settings.
8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
9
10
11 # Load packages -----------------------------------------------------------
12
13 suppressPackageStartupMessages({
14 library(dplyr)
15 library(ggplot2)
16 library(ggrepel)
17 })
18
19
20 # Import data ------------------------------------------------------------
21
22 # Check if header is present by checking if P value column is numeric or not
23
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)
25
26 first_pvalue <- first_line[, 3]
27
28 if (is.numeric(first_pvalue)) {
29 print("No header row detected")
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)
31 } else {
32 print("Header row detected")
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)
34 }
35
36
37 # Format data ------------------------------------------------------------
38
39 # Create columns from the column numbers specified
40 results <- results %>% mutate(fdr = .[[4]],
41 pvalue = .[[3]],
42 logfc = .[[2]],
43 labels = .[[1]])
44
45 # Get names for legend
46 down <- unlist(strsplit('Down,Not Sig,Up', split = ","))[1]
47 notsig <- unlist(strsplit('Down,Not Sig,Up', split = ","))[2]
48 up <- unlist(strsplit('Down,Not Sig,Up', split = ","))[3]
49
50 # Set colours
51 colours <- setNames(c("cornflowerblue", "grey", "firebrick"), c(down, notsig, up))
52
53 # Create significant (sig) column
54 results <- mutate(results, sig = case_when(
55 fdr < 0.05 & logfc > 0.0 ~ up,
56 fdr < 0.05 & logfc < -0.0 ~ down,
57 TRUE ~ notsig))
58
59
60 # Specify genes to label --------------------------------------------------
61 labelfile <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpfpemuuun/files/4/2/f/dataset_42fc8a63-f9cc-435b-9bb3-dd106b708cd9.dat')
62 results <- mutate(results, labels = ifelse(labels %in% labelfile[, 1], labels, ""))
63
64
65 # Create plot -------------------------------------------------------------
66
67 pdf("out.pdf")
68 p <- ggplot(results, aes(x = logfc, y = -log10(pvalue))) +
69 geom_point(aes(colour = sig)) +
70 scale_color_manual(values = colours) +
71 scale_fill_manual(values = colours) +
72 theme(panel.grid.major = element_blank(),
73 panel.grid.minor = element_blank(),
74 panel.background = element_blank(),
75 axis.line = element_line(colour = "black"),
76 legend.key = element_blank())
77
78
79
80
81
82
83 # Set legend title
84 p <- p + labs(colour = "")
85
86 # Add gene labels in boxes
87 p <- p + geom_label_repel(aes(label = labels, fill = sig),
88 segment.colour = "black",
89 colour = "white",
90 min.segment.length = 0,
91 show.legend = FALSE)
92
93 print(p)
94 dev.off()
95
96
97 # Save RData -------------------------------------------------------------
98 save.image(file="volcanoplot.RData")
99
100
101 # R and Package versions -------------------------------------------------
102 sessionInfo()
103