Mercurial > repos > artbio > high_dim_heatmap

annotate heatmap.xml @ 1:e298f66f5d8c 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/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
author artbio
date Tue, 26 Oct 2021 10:22:01 +0000
parents 5182b74b6435
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
1 <tool id="high_dim_heatmap" name="Plot heatmap" version="1.2.0">
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
2 <description>with high number of rows</description>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
3 <requirements>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
4 <requirement type="package" version="3.0.1">r-gplots</requirement>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
5 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
6 </requirements>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
8 cat '$script' &&
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
9 Rscript '$script'
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
10 ]]></command>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
11 <configfiles>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
12 <configfile name="script"><![CDATA[
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
13 ## Setup R error handling to go to stderr
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
14 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
15
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
16 ## Unify locale settings
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
17 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
18
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
19 ## Import library
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
20 library("RColorBrewer")
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
21 library("gplots")
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
22
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
23 input <- read.delim('$input1', sep='\t', header=TRUE)
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
24
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
25 mat_input <- data.matrix(input[, 2:ncol(input)])
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
26 rownames(mat_input) <- input[, 1]
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
27
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
28 #if $transform == "none"
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
29 linput <- mat_input
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
30 #elif $transform == "log2"
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
31 linput <- log2(mat_input)
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
32 #elif $transform == "log2plus1"
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
33 linput <- log2(mat_input + 1)
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
34 #elif $transform == "log10"
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
35 linput <- log10(mat_input)
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
36 #elif $transform == "log10plus1"
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
37 linput <- log10(mat_input + 1)
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
38 #end if
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
39
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
40 #if $colorscheme == "whrd"
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
41 colfunc <- colorRampPalette(c("white", "red"))
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
42 #elif $colorscheme == "whblu"
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
43 colfunc <- colorRampPalette(c("white", "blue"))
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
44 #elif $colorscheme == "blwhre"
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
45 colfunc <- colorRampPalette(c("blue","white", "red"))
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
46 #elif $colorscheme == "yeblu"
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
47 colfunc <- colorRampPalette(c("lightyellow", "royalblue4"))
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
48 #end if
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
49
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
50 #if $labels== "both"
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
51 rlabs = NULL
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
52 clabs = NULL
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
53 #elif $labels== "rows"
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
54 rlabs = NULL
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
55 clabs = FALSE
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
56 #elif $labels== "columns"
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
57 rlabs = FALSE
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
58 clabs = NULL
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
59 #elif $labels== "none"
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
60 rlabs = FALSE
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
61 clabs = FALSE
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
62 #end if
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
63
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
64 pdf(file = '$output1', paper = 'special', height = $height)
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
65 par(cex.main = $title_size)
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
66
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
67 #if $cluster_cond.cluster:
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
68 hclust_fun = function(x) hclust(x, method = '$cluster_cond.clustering')
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
69 dist_fun = function(x) dist(x, method = '$cluster_cond.distance')
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
70 #if $cluster_cond.cluster_cols_rows == "rows":
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
71 heatmap.2(linput, dendrogram="row", Colv = FALSE, Rowv = TRUE,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
72 distfun = dist_fun, hclustfun = hclust_fun, scale = '$scale', labRow = rlabs,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
73 labCol = clabs, col = colfunc(50), trace = "none", density.info = "none",
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
74 margins = c(8,8), main = '$title', key.xlab = '$key', keysize = 1,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
75 cexCol = 0.8, cexRow = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
76 #elif $cluster_cond.cluster_cols_rows == "columns":
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
77 heatmap.2(linput, dendrogram = "column", Colv = TRUE, Rowv = FALSE,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
78 distfun = dist_fun, hclustfun = hclust_fun, scale = '$scale', labRow = rlabs,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
79 labCol = clabs, col = colfunc(50), trace = "none", density.info = "none",
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
80 margins = c(8,8), main = '$title', key.xlab = '$key', keysize = 1,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
81 cexCol = 0.8, cexRow = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
82 #else
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
83 heatmap.2(linput,
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
84 distfun = dist_fun, hclustfun = hclust_fun, scale = '$scale', labRow = rlabs,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
85 labCol = clabs, col = colfunc(50), trace = "none", density.info = "none",
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
86 margins = c(8,8), main = '$title', key.xlab = '$key', keysize = 1,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
87 cexCol = 0.8, cexRow = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
88 #end if
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
89 #else
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
90 heatmap.2(linput,
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
91 dendrogram = "none", Colv = FALSE, Rowv = FALSE, scale = '$scale', labRow = rlabs,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
92 labCol = clabs, col = colfunc(50), trace="none", density.info = "none",
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
93 margins = c(8,8), main = '$title', key.xlab = '$key', keysize = 1, cexCol = 0.8,
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
94 cexRow = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
95 #end if
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
96
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
97 dev.off()
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
98 ]]></configfile>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
99 </configfiles>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
100
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
101 <inputs>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
102 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
103 <param name="title" type="text" format="txt" label="Plot title"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
104 <param name="key" type="text" format="txt" label="key title"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
105 <param name="transform" type="select" label="Data transformation">
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
106 <option value="none">Plot the data as it is</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
107 <option value="log2">Log2(value) transform my data</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
108 <option value="log2plus1">Log2(value+1) transform my data</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
109 <option value="log10">Log10(value) transform my data</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
110 <option value="log10plus1">Log10(value+1) transform my data</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
111 </param>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
112 <conditional name="cluster_cond">
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
113 <param name="cluster" type="select" label="Enable data clustering">
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
114 <option value="true">Yes</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
115 <option value="">No</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
116 </param>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
117 <when value="true">
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
118 <param name="cluster_cols_rows" type="select" label="Clustering columns and rows">
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
119 <option value="both" selected="true">Cluster rows and columns</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
120 <option value="rows">Cluster rows and not columns</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
121 <option value="columns">Cluster columns and not rows</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
122 </param>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
123 <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" >
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
124 <option value="euclidean" selected="true">Euclidean</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
125 <option value="maximum">Maximum</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
126 </param>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
127 <param name="clustering" type="select" label="Clustering method" help="The method used to compute the hierarchical clustering. Default: Complete" >
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
128 <option value="complete" selected="true">Complete</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
129 <option value="average">Average</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
130 </param>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
131 </when>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
132 <when value=""/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
133 </conditional>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
134 <param name="labels" type="select" label="Labeling columns and rows" >
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
135 <option value="both" selected="true">Label my columns and rows</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
136 <option value="rows">Label rows and not columns</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
137 <option value="columns">Label columns and not rows</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
138 <option value="none">Do not label rows or columns</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
139 </param>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
140 <param name="colorscheme" type="select" label="Coloring groups" >
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
141 <option value="whrd" selected="true">White to red</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
142 <option value="whblu">White to blue</option>
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
143 <option value="yeblu">Yellow to blue</option>
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
144 <option value="blwhre">Blue to white to red</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
145 </param>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
146 <param name="scale" type="select" label="Data scaling" >
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
147 <option value="none" selected="true">Do not scale my data</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
148 <option value="row">Scale my data by row</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
149 <option value="column">Scale my data by column</option>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
150 </param>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
151
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
152 <param name="title_size" type="float" label="tweak main title size" value="1" />
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
153 <param name="height" type="float" label="tweak plot height" value="7" />
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
154 <param name="rowfontsize" type="float" label="tweak row label size" value="0.8" />
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
155 <param name="lineheight" type="integer" label="tweak line height" value="4" />
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
156 </inputs>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
157 <outputs>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
158 <data name="output1" format="pdf"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
159 </outputs>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
160 <tests>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
161 <test>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
162 <param name="input1" value="mtcars.txt"/>
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
163 <param name="title" value="This is a pretty long title"/>
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
164 <param name="cluster" value="true"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
165 <output name="output1" file="result1.pdf"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
166 </test>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
167 <test>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
168 <param name="input1" value="mtcars.txt"/>
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
169 <param name="title" value="This is a pretty long title"/>
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
170 <param name="cluster" value=""/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
171 <output name="output1" file="result2.pdf"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
172 </test>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
173 <test>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
174 <param name="input1" value="complex_table.tsv"/>
1
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
175 <param name="title" value="This is a pretty long title for a complex plot"/>
e298f66f5d8c "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 0
diff changeset
176 <param name="title_size" value="0.7"/>
0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
177 <param name="transform" value="log2plus1"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
178 <param name="cluster" value=""/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
179 <param name="colorscheme" value="blwhre"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
180 <param name="height" value="21"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
181 <param name="rowfontsize" value="0.4"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
182 <param name="lineheight" value="15"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
183 <output name="output1" file="complex_result1.pdf"/>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
184 </test>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
185 </tests>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
186 <help><![CDATA[
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
187 This tool employs the heatmap.2 function from the R gplots package and will generate a
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
188 heatmap of your data. If clustering is enabled, the heatmap uses the Euclidean distance
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
189 method and the Complete hierarchical clustering method by default.
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
190
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
191 Input data should have row labels in the first column and column labels. For example,
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
192 the row labels (the first column) should represent gene IDs and the column labels should
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
193 represent sample IDs.
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
194
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
195 To adapt heatmap.2 to high number of lines, tweak the parameters:
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
196
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
197 - `tweak plot height`. By default 7 (inches), this can be increased to 14, 21, 28, etc..
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
198 - `tweak row label size`. By default 0.8. This is usually diminished to 0.3, 0.1, etc to
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
199 adapt the label font to high number of rows
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
200 - `tweak line height`. By default 4. This is a metric to define the relative size of the
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
201 heatmap panel in the plot layout. This is a bit tricky to adjust, but should be adapted
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
202 when plot height is increased (typically to 8, 10, 15, etc...)
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
203
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
204 For instance, upload the dataset
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
205 https://raw.githubusercontent.com/ARTbio/tools-artbio/master/tools/high_dim_heatmap/test-data/complex_table.tsv
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
206 to your account and test this tools with:
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
207
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
208 - `tweak plot height` : 21.0
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
209 - `tweak row label size`: 0.4
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
210 - `tweak line height`: 14
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
211
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
212
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
213 ]]></help>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
214 <citations>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
215 </citations>
5182b74b6435 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
216 </tool>