Mercurial > repos > iuc > dexseq
annotate plotdexseq.R @ 11:9a7c5b6d8f1e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
author | iuc |
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date | Tue, 02 Apr 2024 12:59:54 +0000 |
parents | df929f257179 |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
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1 ## Setup R error handling to go to stderr |
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df929f257179
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
iuc
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2 options(show.error.messages = FALSE, error = function() { |
df929f257179
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
iuc
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3 cat(geterrmessage(), file = stderr()) |
df929f257179
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
iuc
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4 q("no", 1, FALSE) |
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62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
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5 }) |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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7 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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8 |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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9 suppressPackageStartupMessages({ |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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10 library("DEXSeq") |
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62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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11 library("getopt") |
5
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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12 }) |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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13 |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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14 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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15 args <- commandArgs(trailingOnly = TRUE) |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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16 |
11
9a7c5b6d8f1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
iuc
parents:
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17 # get options, using the spec as defined by the enclosed list. |
9a7c5b6d8f1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
iuc
parents:
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18 # we read the options from the default: commandArgs(TRUE). |
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62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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19 spec <- matrix(c( |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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20 "rdata", "r", 1, "character", |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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21 "primaryfactor", "p", 1, "character", |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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22 "geneid", "g", 1, "character", |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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23 "genefile", "f", 1, "character", |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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24 "fdr", "c", 1, "double", |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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25 "transcripts", "t", 1, "logical", |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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26 "names", "a", 1, "logical", |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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27 "normcounts", "n", 1, "logical", |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
5
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28 "splicing", "s", 1, "logical" |
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df929f257179
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
iuc
parents:
7
diff
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29 ), byrow = TRUE, ncol = 4) |
df929f257179
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
iuc
parents:
7
diff
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30 opt <- getopt(spec) |
5
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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31 |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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32 res <- readRDS(opt$rdata) |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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33 |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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34 if (!is.null(opt$genefile)) { |
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62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
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35 genes <- read.delim(opt$genefile, header = FALSE) |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
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36 genes <- genes[, 1] |
5
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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37 } else { |
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62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
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38 genes <- opt$geneid |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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39 } |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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40 |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
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41 pdf("plot.pdf") |
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62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
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42 for (i in genes) { |
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9a7c5b6d8f1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
iuc
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43 plotDEXSeq(res, i, |
9a7c5b6d8f1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
iuc
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44 FDR = opt$fdr, fitExpToVar = opt$primaryfactor, |
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62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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45 norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing, |
62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
iuc
parents:
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46 displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE, |
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9a7c5b6d8f1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
iuc
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47 color = NULL, color.samples = NULL, transcriptDb = NULL |
9a7c5b6d8f1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
iuc
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48 ) |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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49 } |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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50 dev.off() |
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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51 |
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62adf13b86ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
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52 sessionInfo() |