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comparison heatmap.xml @ 0:22d5d811dc37 draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
author artbio
date Sat, 20 Jul 2019 17:55:20 -0400
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children 58b36ae7baca
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-1:000000000000 0:22d5d811dc37
1 <tool id="high_dim_heatmap" name="Plot heatmap" version="1.0.0">
2 <description>with high number of rows</description>
3 <requirements>
4 <requirement type="package" version="3.0.1">r-gplots</requirement>
5 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 cat '$script' &&
9 Rscript '$script'
10 ]]></command>
11 <configfiles>
12 <configfile name="script"><![CDATA[
13 ## Setup R error handling to go to stderr
14 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
15
16 ## Unify locale settings
17 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
18
19 ## Import library
20 library("RColorBrewer")
21 library("gplots")
22
23 input <- read.delim('$input1', sep='\t', header=TRUE)
24
25 mat_input <- data.matrix(input[,2:ncol(input)])
26 rownames(mat_input) <- input[,1]
27
28 #if $transform == "none"
29 linput <- mat_input
30 #elif $transform == "log2"
31 linput <- log2(mat_input)
32 #elif $transform == "log2plus1"
33 linput <- log2(mat_input+1)
34 #elif $transform == "log10"
35 linput <- log10(mat_input)
36 #elif $transform == "log10plus1"
37 linput <- log10(mat_input+1)
38 #end if
39
40 #if $colorscheme == "whrd"
41 colorscale = colfunc <- colorRampPalette(c("white", "red"))
42 #elif $colorscheme == "whblu"
43 colorscale = colfunc <- colorRampPalette(c("white", "blue"))
44 #elif $colorscheme == "blwhre"
45 colorscale = colfunc <- colorRampPalette(c("blue","white", "red"))
46 #end if
47
48 #if $labels== "both"
49 rlabs = NULL
50 clabs = NULL
51 #elif $labels== "rows"
52 rlabs = NULL
53 clabs = FALSE
54 #elif $labels== "columns"
55 rlabs = FALSE
56 clabs = NULL
57 #elif $labels== "none"
58 rlabs = FALSE
59 clabs = FALSE
60 #end if
61
62 pdf(file='$output1', paper='special', height=$height)
63 colorscale
64
65 #if $cluster_cond.cluster:
66 hclust_fun = function(x) hclust(x, method='$cluster_cond.clustering')
67 dist_fun = function(x) dist(x, method='$cluster_cond.distance')
68 #if $cluster_cond.cluster_cols_rows=="rows":
69 heatmap.2(linput, dendrogram="row", Colv=FALSE, Rowv=TRUE,
70 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
71 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
72 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = $rowfontsize, srtCol=45,
73 lhei=c(1, $lineheight))
74 #elif $cluster_cond.cluster_cols_rows=="columns":
75 heatmap.2(linput, dendrogram="column", Colv=TRUE, Rowv=FALSE,
76 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
77 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
78 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = $rowfontsize, srtCol=45,
79 lhei=c(1, $lineheight))
80 #else
81 heatmap.2(linput,
82 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
83 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
84 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = $rowfontsize, srtCol=45,
85 lhei=c(1, $lineheight))
86 #end if
87 #else
88 heatmap.2(linput,
89 dendrogram="none", Colv=FALSE, Rowv=FALSE, scale = '$scale', labRow = rlabs, labCol = clabs,
90 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
91 main='$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = $rowfontsize, srtCol=45,
92 lhei=c(1, $lineheight))
93 #end if
94
95 dev.off()
96 ]]></configfile>
97 </configfiles>
98
99 <inputs>
100 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/>
101 <param name="title" type="text" format="txt" label="Plot title"/>
102 <param name="key" type="text" format="txt" label="key title"/>
103 <param name="transform" type="select" label="Data transformation">
104 <option value="none">Plot the data as it is</option>
105 <option value="log2">Log2(value) transform my data</option>
106 <option value="log2plus1">Log2(value+1) transform my data</option>
107 <option value="log10">Log10(value) transform my data</option>
108 <option value="log10plus1">Log10(value+1) transform my data</option>
109 </param>
110 <conditional name="cluster_cond">
111 <param name="cluster" type="select" label="Enable data clustering">
112 <option value="true">Yes</option>
113 <option value="">No</option>
114 </param>
115 <when value="true">
116 <param name="cluster_cols_rows" type="select" label="Clustering columns and rows">
117 <option value="both" selected="true">Cluster rows and columns</option>
118 <option value="rows">Cluster rows and not columns</option>
119 <option value="columns">Cluster columns and not rows</option>
120 </param>
121 <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" >
122 <option value="euclidean" selected="true">Euclidean</option>
123 <option value="maximum">Maximum</option>
124 </param>
125 <param name="clustering" type="select" label="Clustering method" help="The method used to compute the hierarchical clustering. Default: Complete" >
126 <option value="complete" selected="true">Complete</option>
127 <option value="average">Average</option>
128 </param>
129 </when>
130 <when value=""/>
131 </conditional>
132 <param name="labels" type="select" label="Labeling columns and rows" >
133 <option value="both" selected="true">Label my columns and rows</option>
134 <option value="rows">Label rows and not columns</option>
135 <option value="columns">Label columns and not rows</option>
136 <option value="none">Do not label rows or columns</option>
137 </param>
138 <param name="colorscheme" type="select" label="Coloring groups" >
139 <option value="whrd" selected="true">White to red</option>
140 <option value="whblu">White to blue</option>
141 <option value="blwhre">Blue to white to red</option>
142 </param>
143 <param name="scale" type="select" label="Data scaling" >
144 <option value="none" selected="true">Do not scale my data</option>
145 <option value="row">Scale my data by row</option>
146 <option value="column">Scale my data by column</option>
147 </param>
148
149 <param name="height" type="float" label="tweak plot height" value="7" />
150 <param name="rowfontsize" type="float" label="tweak row label size" value="0.8" />
151 <param name="lineheight" type="integer" label="tweak line height" value="4" />
152 </inputs>
153 <outputs>
154 <data name="output1" format="pdf"/>
155 </outputs>
156 <tests>
157 <test>
158 <param name="input1" value="mtcars.txt"/>
159 <param name="cluster" value="true"/>
160 <output name="output1" file="result1.pdf"/>
161 </test>
162 <test>
163 <param name="input1" value="mtcars.txt"/>
164 <param name="cluster" value=""/>
165 <output name="output1" file="result2.pdf"/>
166 </test>
167 <test>
168 <param name="input1" value="complex_table.tsv"/>
169 <param name="transform" value="log2plus1"/>
170 <param name="cluster" value=""/>
171 <param name="colorscheme" value="blwhre"/>
172 <param name="height" value="21"/>
173 <param name="rowfontsize" value="0.4"/>
174 <param name="lineheight" value="15"/>
175 <output name="output1" file="complex_result1.pdf"/>
176 </test>
177 </tests>
178 <help><![CDATA[
179 This tool employs the heatmap.2 function from the R gplots package and will generate a
180 heatmap of your data. If clustering is enabled, the heatmap uses the Euclidean distance
181 method and the Complete hierarchical clustering method by default.
182
183 Input data should have row labels in the first column and column labels. For example,
184 the row labels (the first column) should represent gene IDs and the column labels should
185 represent sample IDs.
186
187 To adapt heatmap.2 to high number of lines, tweak the parameters:
188
189 - `tweak plot height`. By default 7 (inches), this can be increased to 14, 21, 28, etc..
190 - `tweak row label size`. By default 0.8. This is usually diminished to 0.3, 0.1, etc to
191 adapt the label font to high number of rows
192 - `tweak line height`. By default 4. This is a metric to define the relative size of the
193 heatmap panel in the plot layout. This is a bit tricky to adjust, but should be adapted
194 when plot height is increased (typically to 8, 10, 15, etc...)
195
196 For instance, upload the dataset
197 https://raw.githubusercontent.com/ARTbio/tools-artbio/master/tools/high_dim_heatmap/test-data/complex_table.tsv
198 to your account and test this tools with:
199
200 - `tweak plot height` : 21.0
201 - `tweak row label size`: 0.4
202 - `tweak line height`: 14
203
204
205 ]]></help>
206 <citations>
207 </citations>
208 </tool>