Mercurial > repos > iuc > volcanoplot

annotate test-data/out.rscript @ 7:49456dafcd83 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 060f6734402e7d2eced6227663cc61d2cb865ae5
author iuc
date Mon, 09 Dec 2024 16:04:08 +0000
parents ce288ae050c1
children
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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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10 # Galaxy settings end -----------------------------------------------------
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12 # Load packages -----------------------------------------------------------
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14 suppressPackageStartupMessages({
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15 library(dplyr)
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16 library(ggplot2)
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17 library(ggrepel)
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18 })
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21 # Import data ------------------------------------------------------------
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23 results <- read.delim('/tmp/tmpl4o1f_bf/files/5/2/5/dataset_52538741-d085-42da-817b-263bd4f7cf98.dat', header = TRUE)
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26 # Format data ------------------------------------------------------------
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28 # Create columns from the column numbers specified and use the existing category_symbol column for shapes
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29 results <- results %>% mutate(
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30 fdr = .[[4]],
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31 pvalue = .[[3]],
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32 logfc = .[[2]],
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33 labels = .[[1]],
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34 )
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36 # Check if shape_col is provided
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38 # Get names for legend
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39 down <- unlist(strsplit('Down,Not Sig,Up', split = ","))[1]
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40 notsig <- unlist(strsplit('Down,Not Sig,Up', split = ","))[2]
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41 up <- unlist(strsplit('Down,Not Sig,Up', split = ","))[3]
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43 # Set colours
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44 colours <- setNames(c("cornflowerblue", "grey", "firebrick"), c(down, notsig, up))
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46 # Create significant (sig) column
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47 results <- mutate(results, sig = case_when(
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48 fdr < 0.05 & logfc > 0.0 ~ up,
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49 fdr < 0.05 & logfc < -0.0 ~ down,
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50 TRUE ~ notsig))
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53 # Specify genes to label --------------------------------------------------
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55 # Import file with genes of interest
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56 labelfile <- read.delim('/tmp/tmpl4o1f_bf/files/5/d/4/dataset_5d401b02-f6af-4ed9-b853-992fd4a4d044.dat', header = TRUE)
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58 # Label the genes of interest in results table
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59 results <- mutate(results, labels = ifelse(labels %in% labelfile[, 1], labels, ""))
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63 # Create plot -------------------------------------------------------------
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65 # Open file to save plot as PDF
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66 pdf("volcano_plot.pdf")
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68 # Set up base plot with faceting by category_symbol instead of shapes
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69 p <- ggplot(data = results, aes(x = logfc, y = -log10(pvalue))) +
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70 scale_color_manual(values = colours) +
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71 theme(panel.grid.major = element_blank(),
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72 panel.grid.minor = element_blank(),
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73 panel.background = element_blank(),
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74 axis.line = element_line(colour = "black"),
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75 legend.key = element_blank())
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77 # Conditional logic to use either shape or facet based on user selection
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78 p <- p + geom_point(aes(colour = sig)) #only add color
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80 # Add gene labels
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81 p <- p + geom_text_repel(data = filter(results, labels != ""), aes(label = labels),
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82 min.segment.length = 0,
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83 max.overlaps = Inf,
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84 show.legend = FALSE)
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91 # Set legend title
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92 p <- p + theme(legend.title = element_blank())
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94 # Print plot
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95 print(p)
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97 # Close PDF graphics device
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98 dev.off()
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101 # R and Package versions -------------------------------------------------
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102 sessionInfo()
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