Mercurial > repos > iuc > volcanoplot

annotate volcanoplot.xml @ 8:2f557f6abbfb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 a363ba287b88
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
1 <tool id="volcanoplot" name="Volcano Plot" version="0.0.6" profile="20.09">
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
2 <description>create a volcano plot</description>
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
3 <edam_topics>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
4 <edam_topic>topic_0092</edam_topic>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
5 </edam_topics>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
6 <edam_operations>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
7 <edam_operation>operation_0337</edam_operation>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
8 </edam_operations>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
9 <requirements>
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
10 <requirement type="package" version="3.3.3">r-ggplot2</requirement>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
11 <requirement type="package" version="0.9.1">r-ggrepel</requirement>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
12 <requirement type="package" version="1.0.6">r-dplyr</requirement>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
13 </requirements>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
14 <version_command><![CDATA[
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
15 echo $(R --version | grep version | grep -v GNU)", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggrepel version" $(R --vanilla --slave -e "library(ggrepel); cat(sessionInfo()\$otherPkgs\$ggrepel\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
16 ]]></version_command>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
17 <command detect_errors="exit_code"><![CDATA[
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
18 #if $out_options.rscript_out:
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
19 cp '${volcanoplot_script}' rscript.txt &&
3
6d532d760950 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 16205b1cd782c5a4f7c08af7d4ee50dc5903418b
iuc
parents: 1
diff changeset
20 #end if
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
21 Rscript '${volcanoplot_script}'
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
22 ]]></command>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
23 <configfiles>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
24 <configfile name="volcanoplot_script"><![CDATA[
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
25 # Galaxy settings start ---------------------------------------------------
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
26
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
27 # setup R error handling to go to stderr
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
28 options(show.error.messages = F, error = function() {cat(geterrmessage(), file = stderr()); q("no", 1, F)})
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
29
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
30 # we need that to not crash galaxy with an UTF8 error on German LC settings.
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
31 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
32
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
33 # Galaxy settings end -----------------------------------------------------
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
34
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
35 # Load packages -----------------------------------------------------------
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
36
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
37 suppressPackageStartupMessages({
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
38 library(dplyr)
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
39 library(ggplot2)
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
40 library(ggrepel)
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
41 })
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
42
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
43
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
44 # Import data ------------------------------------------------------------
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
45
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
46 #if $header == "yes"
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
47 results <- read.delim('$input', header = TRUE)
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
48
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
49 #elif $header == "no"
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
50 results <- read.delim('$input', header = FALSE)
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
51
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
52 #else
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
53 # Auto-detect header by checking if P value column is numeric or not
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
54 first_line <- read.delim('$input', header = FALSE, nrow = 1)
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
55 first_pvalue <- first_line[, $pval_col]
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
56 if (is.numeric(first_pvalue)) {
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
57 print("No header row detected")
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
58 results <- read.delim('$input', header = FALSE)
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
59 } else {
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
60 print("Header row detected")
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
61 results <- read.delim('$input', header = TRUE)
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
62 }
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
63 #end if
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
64
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
65 # Format data ------------------------------------------------------------
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
66
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
67 # Create columns from the column numbers specified
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
68 results <- results %>% mutate(fdr = .[[$fdr_col]],
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
69 pvalue = .[[$pval_col]],
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
70 logfc = .[[$lfc_col]],
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
71 labels = .[[$label_col]])
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
72
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
73 # Get names for legend
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
74 down <- unlist(strsplit('$plot_options.legend_labs', split = ","))[1]
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
75 notsig <- unlist(strsplit('$plot_options.legend_labs', split = ","))[2]
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
76 up <- unlist(strsplit('$plot_options.legend_labs', split = ","))[3]
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
77
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
78 # Set colours
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
79 colours <- setNames(c("cornflowerblue", "grey", "firebrick"), c(down, notsig, up))
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
80
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
81 # Create significant (sig) column
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
82 results <- mutate(results, sig = case_when(
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
83 fdr < $signif_thresh & logfc > $lfc_thresh ~ up,
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
84 fdr < $signif_thresh & logfc < -$lfc_thresh ~ down,
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
85 TRUE ~ notsig))
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
86
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
87 ## R code below is left aligned for R script output
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
88
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
89 #if $labels.label_select != "none"
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
90 # Specify genes to label --------------------------------------------------
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
91
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
92 #if $labels.label_select == "file"
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
93 # Import file with genes of interest
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
94 labelfile <- read.delim('$labels.label_file', header = TRUE)
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
95
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
96 # Label the genes of interest in results table
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
97 results <- mutate(results, labels = ifelse(labels %in% labelfile[, 1], labels, ""))
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
98
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
99 #elif $labels.label_select == "signif"
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
100 #if not $labels.top_num
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
101 # Label all significant genes in results table
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
102 results <- mutate(results, labels=ifelse(sig != notsig, labels, ""))
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
103
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
104 #elif $labels.top_num > 0
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
105 # Get top genes by P value
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
106 top <- slice_min(results, order_by = pvalue, n = $labels.top_num)
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
107
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
108 # Extract into vector
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
109 toplabels <- pull(top, labels)
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
110
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
111 # Label just the top genes in results table
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
112 results <- mutate(results, labels = ifelse(labels %in% toplabels, labels, ""))
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
113 #end if
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
114 #end if
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
115 #end if
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
116
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
117
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
118 # Create plot -------------------------------------------------------------
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
119
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
120 # Open file to save plot as PDF
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
121 pdf("volcano_plot.pdf")
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
122
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
123 # Set up base plot
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
124 p <- ggplot(data = results, aes(x = logfc, y = -log10(pvalue))) +
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
125 geom_point(aes(colour = sig)) +
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
126 scale_color_manual(values = colours) +
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
127 theme(panel.grid.major = element_blank(),
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
128 panel.grid.minor = element_blank(),
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
129 panel.background = element_blank(),
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
130 axis.line = element_line(colour = "black"),
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
131 legend.key = element_blank())
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
132
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
133 #if $labels.label_select != "none"
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
134 # Add gene labels
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
135 #if $plot_options.boxes
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
136 p <- p + geom_label_repel(data = filter(results, labels != ""), aes(label = labels),
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
137 min.segment.length = 0,
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
138 max.overlaps = Inf,
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
139 show.legend = FALSE)
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
140 #else
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
141 p <- p + geom_text_repel(data = filter(results, labels != ""), aes(label = labels),
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
142 min.segment.length = 0,
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
143 max.overlaps = Inf,
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
144 show.legend = FALSE)
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
145 #end if
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
146 #end if
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
147
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
148 #if $plot_options.title:
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
149 p <- p + ggtitle('$plot_options.title')
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
150 #end if
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
151
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
152 #if $plot_options.xlab:
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
153 p <- p + xlab('$plot_options.xlab')
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
154 #end if
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
155
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
156 #if $plot_options.ylab:
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
157 p <- p + ylab('$plot_options.ylab')
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
158 #end if
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
159
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
160 #if $plot_options.xmin and $plot_options.xmax:
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
161 p <- p + xlim($plot_options.xmin, $plot_options.xmax)
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
162 #end if
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
163
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
164 #if $plot_options.ymax:
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
165 p <- p + ylim(0, $plot_options.ymax)
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
166 #end if
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
167
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
168 # Set legend title
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
169 #if $plot_options.legend:
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
170 p <- p + guides(color = guide_legend(title = '$plot_options.legend'))
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
171 #else
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
172 p <- p + theme(legend.title = element_blank())
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
173 #end if
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
174
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
175 # Print plot
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
176 print(p)
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
177
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
178 # Close PDF graphics device
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
179 dev.off()
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
180
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
181
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
182 # R and Package versions -------------------------------------------------
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
183 sessionInfo()
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
184
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
185 ]]></configfile>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
186 </configfiles>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
187 <inputs>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
188 <param name="input" type="data" format="tabular" label="Specify an input file" />
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
189 <param name="header" type="select" label="File has header?" help="Does the differentially expressed results file contain a header row. The tool can auto-detect by checking if the first row in the P value column is a number or not. Default: Auto-detect">
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
190 <option value="auto" selected="True">Auto-detect</option>
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
191 <option value="yes">Yes</option>
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
192 <option value="no">No</option>
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
193 </param>
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
194 <param name="fdr_col" type="data_column" data_ref="input" label="FDR (adjusted P value) column number" />
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
195 <param name="pval_col" type="data_column" data_ref="input" label="P value (raw) column number" />
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
196 <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change column number" />
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
197 <param name="label_col" type="data_column" data_ref="input" label="Labels column number" />
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
198 <param name="signif_thresh" type="float" max="1" value="0.05" label="Significance threshold" help="Default: 0.05"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
199 <param name="lfc_thresh" type="float" value="0" label="LogFC threshold to colour" help="Default: 0"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
200 <conditional name="labels">
1
7b7303fa20e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit c2b155f1fd4470ddecb5bd1c6e2c54dd46bfeaed
iuc
parents: 0
diff changeset
201 <param name="label_select" type="select" label="Points to label" help="Select to label significant points or input labels from file. Default: None">
7b7303fa20e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit c2b155f1fd4470ddecb5bd1c6e2c54dd46bfeaed
iuc
parents: 0
diff changeset
202 <option value="none" selected="True">None</option>
7b7303fa20e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit c2b155f1fd4470ddecb5bd1c6e2c54dd46bfeaed
iuc
parents: 0
diff changeset
203 <option value="signif">Significant</option>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
204 <option value="file">Input from file</option>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
205 </param>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
206 <when value="signif">
1
7b7303fa20e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit c2b155f1fd4470ddecb5bd1c6e2c54dd46bfeaed
iuc
parents: 0
diff changeset
207 <param name="top_num" type="integer" optional="True" label="Only label top most significant" help="Specify the top number of points to label by P value significance. If no number is specified, all points that pass the FDR and Log Fold Change thresholds will be labelled."/>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
208 </when>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
209 <when value="file">
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
210 <param name="label_file" type="data" format="tabular" label="File of labels"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
211 </when>
4
73b8cb5bddcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e8c104fae4904d9c3c35834ac37ee17cf8e49bb9
iuc
parents: 3
diff changeset
212 <when value="none" />
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
213 </conditional>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
214 <section name="plot_options" expanded="false" title="Plot Options">
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
215 <param name="boxes" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Label Boxes" help="If this is set to Yes, the labels for the points will be in boxes. Default: No"/>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
216 <param name="title" type="text" optional="True" label="Plot title"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
217 <param name="xlab" type="text" optional="True" label="Label for x axis"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
218 <param name="ylab" type="text" optional="True" label="Label for y axis"/>
3
6d532d760950 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 16205b1cd782c5a4f7c08af7d4ee50dc5903418b
iuc
parents: 1
diff changeset
219 <param name="xmin" type="float" optional="True" label="Minimum value for x axis" help="To customise the x axis limits, specify both minimum and maximum values. Leave empty for automatic values."/>
6d532d760950 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 16205b1cd782c5a4f7c08af7d4ee50dc5903418b
iuc
parents: 1
diff changeset
220 <param name="xmax" type="float" optional="True" label="Maximum value for x axis" help="To customise the x axis limits, specify both minimum and maximum values. Leave empty for automatic values."/>
6d532d760950 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 16205b1cd782c5a4f7c08af7d4ee50dc5903418b
iuc
parents: 1
diff changeset
221 <param name="ymax" type="float" optional="True" label="Maximum value for y axis" help="To customise the y axis upper limit, specify the maximum value, the minimum will be 0. Leave empty for automatic value."/>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
222 <param name="legend" type="text" optional="True" label="Label for Legend Title"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
223 <param name="legend_labs" type="text" value="Down,Not Sig,Up" label="Labels for Legend" help="Labels in the legend can be specified. Default: Down,Not Sig,Up"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
224 </section>
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
225 <section name="out_options" expanded="false" title="Output Options">
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
226 <param name="rscript_out" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?"
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
227 help="Output the R code used by the tool. Can edit in R if you want to customise the plot further. Default: No"/>
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
228 </section>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
229 </inputs>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
230 <outputs>
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
231 <data name="plot" format="pdf" from_work_dir="volcano_plot.pdf" label="${tool.name} on ${on_string}: PDF"/>
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
232 <data name="rscript" format="txt" from_work_dir="rscript.txt" label="${tool.name} on ${on_string}: Rscript">
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
233 <filter>out_options['rscript_out']</filter>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
234 </data>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
235 </outputs>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
236 <tests>
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
237 <test expect_num_outputs="1">
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
238 <!-- Ensure default output works -->
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
239 <param name="input" ftype="tabular" value="input.tab"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
240 <param name="fdr_col" value="4" />
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
241 <param name="pval_col" value="3" />
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
242 <param name="lfc_col" value="2" />
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
243 <param name="label_col" value="1" />
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
244 <param name="lfc_thresh" value="0" />
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
245 <output name="plot">
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
246 <assert_contents>
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
247 <has_size value= "933451" delta="1000" />
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
248 </assert_contents>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
249 </output>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
250 </test>
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
251 <test expect_num_outputs="1">
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
252 <!-- Ensure input labels and plot options work -->
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
253 <param name="input" ftype="tabular" value="input.tab"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
254 <param name="fdr_col" value="4" />
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
255 <param name="pval_col" value="3" />
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
256 <param name="lfc_col" value="2" />
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
257 <param name="label_col" value="1" />
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
258 <param name="lfc_thresh" value="0" />
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
259 <param name="label_select" value="file"/>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
260 <param name="label_file" ftype="tabular" value="labels.tab" />
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
261 <output name="plot">
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
262 <assert_contents>
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
263 <has_size value= "933830" delta="1000" />
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
264 </assert_contents>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
265 </output>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
266 </test>
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
267 <test expect_num_outputs="2">
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
268 <!-- Ensure rscript output works -->
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
269 <param name="input" ftype="tabular" value="input.tab"/>
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
270 <param name="header" value="yes"/>
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
271 <param name="fdr_col" value="4" />
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
272 <param name="pval_col" value="3" />
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
273 <param name="lfc_col" value="2" />
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
274 <param name="label_col" value="1" />
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
275 <param name="lfc_thresh" value="0" />
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
276 <param name="label_select" value="file"/>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
277 <param name="label_file" ftype="tabular" value="labels.tab" />
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
278 <param name="rscript_out" value="True"/>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
279 <output name="plot">
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
280 <assert_contents>
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
281 <has_size value= "933832" delta="1000" />
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
282 </assert_contents>
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
283 </output>
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
284 <output name="rscript" value= "out.rscript" lines_diff="4"/>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
285 </test>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
286 </tests>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
287 <help><![CDATA[
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
288 .. class:: infomark
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
289
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
290 **What it does**
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
291
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
292 This tool creates a Volcano plot using ggplot2. Points can be labelled via ggrepel. It was inspired by this Getting Genetics Done `blog post`_.
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
293
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
294 In statistics, a `Volcano plot`_ is a type of scatter-plot that is used to quickly identify changes in large data sets composed of replicate data. It plots significance versus fold-change on the y and x axes, respectively. These plots are increasingly common in omic experiments such as genomics, proteomics, and metabolomics where one often has a list of many thousands of replicate data points between two conditions and one wishes to quickly identify the most meaningful changes. A volcano plot combines a measure of statistical significance from a statistical test (e.g., a p value from an ANOVA model) with the magnitude of the change, enabling quick visual identification of those data-points (genes, etc.) that display large magnitude changes that are also statistically significant.
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
295
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
296 A volcano plot is constructed by plotting the negative log of the p value on the y axis (usually base 10). This results in data points with low p values (highly significant) appearing toward the top of the plot. The x axis is the log of the fold change between the two conditions. The log of the fold change is used so that changes in both directions appear equidistant from the center. Plotting points in this way results in two regions of interest in the plot: those points that are found toward the top of the plot that are far to either the left- or right-hand sides. These represent values that display large magnitude fold changes (hence being left or right of center) as well as high statistical significance (hence being toward the top).
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
297
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
298 Source: Wikipedia
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
299
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
300 -----
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
301
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
302 **Inputs**
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
303
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
304 A tabular file containing the columns below (additional columns may be present):
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
305
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
306 * P value
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
307 * FDR / adjusted P value
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
308 * Log fold change
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
309 * Labels (e.g. Gene symbols or IDs)
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
310
1
7b7303fa20e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit c2b155f1fd4470ddecb5bd1c6e2c54dd46bfeaed
iuc
parents: 0
diff changeset
311 All significant points, those meeting the specified FDR and Log Fold Change thresholds, will be coloured, red for upregulated, blue for downregulated. Users can choose to apply labels to the points (such as gene symbols) from the Labels column. To label all significant points, select "Significant" for the **Points to label** option, or to only label the top most significant specify a number under "Only label top most significant". Users can label any points of interest through selecting **Points to label** "Input from file" and providing a tabular labels file. The labels file must contain a header row and have the labels in the first column. These labels must match the labels in the main input file.
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
312
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
313 **Outputs**
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
314
6
83c573f2e73c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"
iuc
parents: 5
diff changeset
315 A PDF containing a Volcano plot like below. The R code can be output through *Output Options* in the tool form.
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
316
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
317 .. image:: $PATH_TO_IMAGES/volcano_plot.png
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
318
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
319 .. _Volcano plot: https://en.wikipedia.org/wiki/Volcano_plot_(statistics)
5
44608d0193ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"
iuc
parents: 4
diff changeset
320 .. _blog post: https://gettinggeneticsdone.blogspot.com/2016/01/
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
321
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
322 ]]></help>
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
323 <citations>
8
2f557f6abbfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 84949ce3d77433f035c14406fccc5bc6beaa7a0d
iuc
parents: 7
diff changeset
324 <citation type="doi">10.1007/978-3-319-24277-4</citation>
0
59ebf2c42c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 7cc1a05f2868f270bf5bdbbd4820ef6f69c9fc8d
iuc
parents:
diff changeset
325 </citations>
7
a363ba287b88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125
iuc
parents: 6
diff changeset
326 </tool>