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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 84949ce3d77433f035c14406fccc5bc6beaa7a0d
author iuc
date Wed, 05 Jun 2024 15:03:07 +0000
parents 83c573f2e73c
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('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmprh4qip75/files/d/2/2/dataset_d2255b46-f0f6-4900-8b9e-bd352e34f303.dat', header = TRUE)
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26 # Format data ------------------------------------------------------------
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28 # Create columns from the column numbers specified
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29 results <- results %>% mutate(fdr = .[[4]],
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30 pvalue = .[[3]],
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31 logfc = .[[2]],
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32 labels = .[[1]])
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34 # Get names for legend
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35 down <- unlist(strsplit('Down,Not Sig,Up', split = ","))[1]
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36 notsig <- unlist(strsplit('Down,Not Sig,Up', split = ","))[2]
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37 up <- unlist(strsplit('Down,Not Sig,Up', split = ","))[3]
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39 # Set colours
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40 colours <- setNames(c("cornflowerblue", "grey", "firebrick"), c(down, notsig, up))
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42 # Create significant (sig) column
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43 results <- mutate(results, sig = case_when(
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44 fdr < 0.05 & logfc > 0.0 ~ up,
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45 fdr < 0.05 & logfc < -0.0 ~ down,
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46 TRUE ~ notsig))
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49 # Specify genes to label --------------------------------------------------
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51 # Import file with genes of interest
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52 labelfile <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmprh4qip75/files/5/e/5/dataset_5e5b8fb0-bf65-438e-9b5b-03a540d9aa5d.dat', header = TRUE)
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54 # Label the genes of interest in results table
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55 results <- mutate(results, labels = ifelse(labels %in% labelfile[, 1], labels, ""))
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59 # Create plot -------------------------------------------------------------
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61 # Open file to save plot as PDF
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62 pdf("volcano_plot.pdf")
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64 # Set up base plot
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65 p <- ggplot(data = results, aes(x = logfc, y = -log10(pvalue))) +
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66 geom_point(aes(colour = sig)) +
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67 scale_color_manual(values = colours) +
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68 theme(panel.grid.major = element_blank(),
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69 panel.grid.minor = element_blank(),
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70 panel.background = element_blank(),
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71 axis.line = element_line(colour = "black"),
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72 legend.key = element_blank())
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74 # Add gene labels
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75 p <- p + geom_text_repel(data = filter(results, labels != ""), aes(label = labels),
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76 min.segment.length = 0,
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77 max.overlaps = Inf,
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78 show.legend = FALSE)
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85 # Set legend title
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86 p <- p + theme(legend.title = element_blank())
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88 # Print plot
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89 print(p)
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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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90
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
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91 # Close PDF graphics device
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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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92 dev.off()
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
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93
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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95 # R and Package versions -------------------------------------------------
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
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96 sessionInfo()
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
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97