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comparison heatmap2.xml @ 5:3b37b1b1c3a7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
author iuc
date Tue, 12 Apr 2022 15:53:40 +0000
parents ca7cb0eaad62
children 566197475670
comparison
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4:ca7cb0eaad62 5:3b37b1b1c3a7
1 <tool id="ggplot2_heatmap2" name="heatmap2" version="@VERSION@"> 1 <tool id="ggplot2_heatmap2" name="heatmap2" version="@VERSION@">
2 <macros> 2 <macros>
3 <token name="@VERSION@">3.0.1</token> 3 <token name="@VERSION@">3.1.1</token>
4 </macros> 4 </macros>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@VERSION@">r-gplots</requirement> 6 <requirement type="package" version="@VERSION@">r-gplots</requirement>
7 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> 7 <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 cat '$script' && 10 cat '$script' &&
11 Rscript '$script' 11 Rscript '$script'
12 ]]></command> 12 ]]></command>
37 linput <- log10(mat_input) 37 linput <- log10(mat_input)
38 #elif $transform == "log10plus1" 38 #elif $transform == "log10plus1"
39 linput <- log10(mat_input+1) 39 linput <- log10(mat_input+1)
40 #end if 40 #end if
41 41
42 #if $colorscheme == "whrd" 42 #if $zscore_cond.zscore == "rows":
43 colorscale = colfunc <- colorRampPalette(c("white", "red")) 43 linput <- t(apply(linput, 1, scale))
44 #elif $colorscheme == "whblu" 44 colnames(linput) <- colnames(input)
45 colorscale = colfunc <- colorRampPalette(c("white", "blue")) 45 rownames(linput) <- input[,1]
46 #elif $colorscheme == "blwhre" 46 scale <- "none"
47 colorscale = colfunc <- colorRampPalette(c("blue","white", "red")) 47 #elif $zscore_cond.zscore == "cols":
48 #end if 48 linput <- apply(linput, 2, scale)
49 49 rownames(linput) <- input[,1]
50 #if $labels== "both" 50 scale <- "none"
51 rlabs = NULL 51 #elif $zscore_cond.zscore == "none":
52 clabs = NULL 52 scale <- "$zscore_cond.scale"
53 #elif $labels== "rows" 53 #end if
54 rlabs = NULL 54
55 clabs = FALSE 55 srtCol <- 45
56 #elif $labels== "columns" 56 #if $labels == "both"
57 rlabs = FALSE 57 rlabs <- NULL
58 clabs = NULL 58 clabs <- NULL
59 #elif $labels== "none" 59 #elif $labels == "rows"
60 rlabs = FALSE 60 rlabs <- NULL
61 clabs = FALSE 61 clabs <- FALSE
62 #end if 62 srtCol <- NULL
63 63 #elif $labels == "columns"
64 pdf(file='$output1') 64 rlabs <- FALSE
65 colorscale 65 clabs <- NULL
66 66 #elif $labels == "none"
67 #if $cluster_cond.cluster: 67 rlabs <- FALSE
68 hclust_fun = function(x) hclust(x, method='$cluster_cond.clustering') 68 clabs <- FALSE
69 dist_fun = function(x) dist(x, method='$cluster_cond.distance') 69 srtCol <- NULL
70 #if $cluster_cond.cluster_cols_rows=="rows": 70 #end if
71 heatmap.2(linput, dendrogram="row", Colv=FALSE, Rowv=TRUE, 71
72 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs, 72 #if $cluster_cond.cluster == "yes":
73 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8), 73 dendrogramtoplot <- "$cluster_cond.cluster_cols_rows"
74 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45) 74 #if $cluster_cond.cluster_cols_rows == "both"
75 #elif $cluster_cond.cluster_cols_rows=="columns": 75 reorder_cols <- TRUE
76 heatmap.2(linput, dendrogram="column", Colv=TRUE, Rowv=FALSE, 76 reorder_rows <- TRUE
77 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs, 77 #elif $cluster_cond.cluster_cols_rows == "row"
78 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8), 78 reorder_cols <- FALSE
79 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45) 79 reorder_rows <- TRUE
80 #else 80 #elif $cluster_cond.cluster_cols_rows == "column"
81 heatmap.2(linput, 81 reorder_cols <- TRUE
82 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs, 82 reorder_rows <- FALSE
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 = 0.8, srtCol=45)
85 #end if 83 #end if
86 #else 84 hclust_fun <- function(x) hclust(x, method='$cluster_cond.clustering')
87 heatmap.2(linput, 85 #if $cluster_cond.distance == 'pearson_correlation':
88 dendrogram="none", Colv=FALSE, Rowv=FALSE, scale = '$scale', labRow = rlabs, labCol = clabs, 86 dist_fun <- function(x) as.dist(1 - cor(t(x)))
89 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8), 87 #elif $cluster_cond.distance == 'spearmann_correlation':
90 main='$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45) 88 dist_fun <- function(x) as.dist(1 - cor(t(x), method="spearman"))
91 #end if 89 #else:
90 dist_fun <- function(x) dist(x, method='$cluster_cond.distance')
91 #end if
92 #else:
93 dendrogramtoplot <- "none"
94 reorder_cols <- FALSE
95 reorder_rows <- FALSE
96 hclust_fun <- hclust
97 dist_fun <- dist
98 #end if
99
100 ncolors <- 50
101 #if $colorchoice.type == "palettes":
102 colused <- brewer.pal(ncolors, "$colorchoice.name")
103 #elif $colorchoice.type == "two"
104 colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2"))(ncolors)
105 #elif $colorchoice.type == "three"
106 colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2", "$colorchoice.color3"))(ncolors)
107 #end if
108
109 #if $image_file_format == "pdf":
110 pdf(file='$output1')
111 #else:
112 png(file='$output1')
113 #end if
114
115 heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
116 distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
117 col=colused, trace="none", density.info = "none", margins=c(8,8),
118 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=srtCol)
92 119
93 dev.off() 120 dev.off()
94 ]]></configfile> 121 ]]></configfile>
95 </configfiles> 122 </configfiles>
96 123
97 <inputs> 124 <inputs>
98 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/> 125 <param name="input1" type="data" format="tabular"
126 label="Input should have column headers - these will be the columns that are plotted and row names."/>
99 <param name="title" type="text" format="txt" label="Plot title"/> 127 <param name="title" type="text" format="txt" label="Plot title"/>
100 <param name="key" type="text" format="txt" label="key title"/> 128 <param name="key" type="text" format="txt" label="key title"/>
101 <param name="transform" type="select" label="Data transformation"> 129 <param name="transform" type="select" label="Data transformation">
102 <option value="none">Plot the data as it is</option> 130 <option value="none">Plot the data as it is</option>
103 <option value="log2">Log2(value) transform my data</option> 131 <option value="log2">Log2(value) transform my data</option>
104 <option value="log2plus1">Log2(value+1) transform my data</option> 132 <option value="log2plus1">Log2(value+1) transform my data</option>
105 <option value="log10">Log10(value) transform my data</option> 133 <option value="log10">Log10(value) transform my data</option>
106 <option value="log10plus1">Log10(value+1) transform my data</option> 134 <option value="log10plus1">Log10(value+1) transform my data</option>
107 </param> 135 </param>
136 <conditional name="zscore_cond">
137 <param name="zscore" type="select" label="Compute z-scores prior to clustering">
138 <option value="none">Do not compute z-scores</option>
139 <option value="rows">Compute on rows</option>
140 <option value="cols">Compute on columns</option>
141 </param>
142 <when value="none">
143 <param name="scale" type="select" label="Scale data on the plot (after clustering)" >
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 </when>
149 <when value="rows"/>
150 <when value="cols"/>
151 </conditional>
108 <conditional name="cluster_cond"> 152 <conditional name="cluster_cond">
109 <param name="cluster" type="select" label="Enable data clustering"> 153 <param name="cluster" type="select" label="Enable data clustering">
110 <option value="true">Yes</option> 154 <option value="yes">Yes</option>
111 <option value="">No</option> 155 <option value="no">No</option>
112 </param> 156 </param>
113 <when value="true"> 157 <when value="yes">
114 <param name="cluster_cols_rows" type="select" label="Clustering columns and rows"> 158 <param name="cluster_cols_rows" type="select" label="Clustering columns and rows">
115 <option value="both" selected="true">Cluster rows and columns</option> 159 <option value="both" selected="true">Cluster rows and columns</option>
116 <option value="rows">Cluster rows and not columns</option> 160 <option value="row">Cluster rows and not columns</option>
117 <option value="columns">Cluster columns and not rows</option> 161 <option value="column">Cluster columns and not rows</option>
118 </param> 162 </param>
119 <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" > 163 <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" >
120 <option value="euclidean" selected="true">Euclidean</option> 164 <option value="euclidean" selected="true">Euclidean</option>
121 <option value="maximum">Maximum</option> 165 <option value="maximum">Maximum</option>
166 <option value="manhattan">Manhattan</option>
167 <option value="canberra">Canberra</option>
168 <option value="binary">Binary</option>
169 <option value="minkowski">Minkowski</option>
170 <option value="pearson_correlation">Pearson's correlation (1 - correlation coefficient)</option>
171 <option value="spearmann_correlation">Spearmann's correlation (1 - correlation coefficient)</option>
122 </param> 172 </param>
123 <param name="clustering" type="select" label="Clustering method" help="The method used to compute the hierarchical clustering. Default: Complete" > 173 <param name="clustering" type="select" label="Clustering method" help="The method used to compute the hierarchical clustering. Default: Complete" >
124 <option value="complete" selected="true">Complete</option> 174 <option value="complete" selected="true">Complete</option>
125 <option value="average">Average</option> 175 <option value="average">Average (= UPGMA)</option>
126 </param> 176 <option value="ward.D">ward.D</option>
127 </when> 177 <option value="ward.D2">ward.D2</option>
128 <when value=""/> 178 <option value="single">single</option>
179 <option value="mcquitty">mcquitty (= WPGMA)</option>
180 <option value="median">median (= WPGMC)</option>
181 <option value="centroid">centroid (= UPGMC)</option>
182 </param>
183 </when>
184 <when value="no"/>
129 </conditional> 185 </conditional>
130 <param name="labels" type="select" label="Labeling columns and rows" > 186 <param name="labels" type="select" label="Labeling columns and rows" >
131 <option value="both" selected="true">Label my columns and rows</option> 187 <option value="both" selected="true">Label my columns and rows</option>
132 <option value="rows">Label rows and not columns</option> 188 <option value="rows">Label rows and not columns</option>
133 <option value="columns">Label columns and not rows</option> 189 <option value="columns">Label columns and not rows</option>
134 <option value="none">Do not label rows or columns</option> 190 <option value="none">Do not label rows or columns</option>
135 </param> 191 </param>
136 <param name="colorscheme" type="select" label="Coloring groups" > 192 <conditional name="colorchoice">
137 <option value="whrd" selected="true">White to red</option> 193 <param name="type" type="select" label="Type of colormap to use">
138 <option value="whblu">White to blue</option> 194 <option value="palettes">RColorBrewer palettes</option>
139 <option value="blwhre">Blue to white to red</option> 195 <option value="two">Gradient with 2 colors</option>
140 </param> 196 <option value="three">Gradient with 3 colors</option>
141 <param name="scale" type="select" label="Data scaling" > 197 </param>
142 <option value="none" selected="true">Do not scale my data</option> 198 <when value="palettes">
143 <option value="row">Scale my data by row</option> 199 <param name="name" type="select" label="Name of the colormap">
144 <option value="column">Scale my data by column</option> 200 <option value="BrBG">BrBG</option>
201 <option value="PiYG">PiYG</option>
202 <option value="PRGn">PRGn</option>
203 <option value="PuOr">PuOr</option>
204 <option value="RdBu">RdBu</option>
205 <option value="RdGy">RdGy</option>
206 <option value="RdYlBu">RdYlBu</option>
207 <option value="RdYlGn">RdYlGn</option>
208 <option value="Spectral">Spectral</option>
209 <option value="Blues">Blues</option>
210 <option value="BuGn">BuGn</option>
211 <option value="BuPu">BuPu</option>
212 <option value="GnBu">GnBu</option>
213 <option value="Greens">Greens</option>
214 <option value="Greys">Greys</option>
215 <option value="Oranges">Oranges</option>
216 <option value="OrRd">OrRd</option>
217 <option value="PuBu">PuBu</option>
218 <option value="PuBuGn">PuBuGn</option>
219 <option value="PuRd">PuRd</option>
220 <option value="Purples">Purples</option>
221 <option value="RdPu">RdPu</option>
222 <option value="Reds">Reds</option>
223 <option value="YlGn">YlGn</option>
224 <option value="YlGnBu">YlGnBu</option>
225 <option value="YlOrBr">YlOrBr</option>
226 <option value="YlOrRd">YlOrRd</option>
227 </param>
228 </when>
229 <when value="two">
230 <param name="color1" type="color" value="#ffffff" label="First color" />
231 <param name="color2" type="color" value="#ff0000" label="Second color" />
232 </when>
233 <when value="three">
234 <param name="color1" type="color" value="#0000ff" label="First color" />
235 <param name="color2" type="color" value="#ffffff" label="Second color" />
236 <param name="color3" type="color" value="#ff0000" label="Third color" />
237 </when>
238 </conditional>
239 <param name="image_file_format" type="select" label="Output format">
240 <option value="pdf">PDF</option>
241 <option value="png">PNG</option>
145 </param> 242 </param>
146 </inputs> 243 </inputs>
147 <outputs> 244 <outputs>
148 <data name="output1" format="pdf"/> 245 <data name="output1" format="pdf">
246 <change_format>
247 <when input="image_file_format" value="png" format="png" />
248 </change_format>
249 </data>
149 </outputs> 250 </outputs>
150 <tests> 251 <tests>
151 <test> 252 <test>
152 <param name="input1" value="mtcars.txt"/> 253 <param name="input1" value="mtcars.txt"/>
153 <param name="cluster" value="true"/> 254 <param name="cluster" value="yes"/>
255 <param name="type" value="two"/>
154 <output name="output1" file="result1.pdf" compare="sim_size"/> 256 <output name="output1" file="result1.pdf" compare="sim_size"/>
155 </test> 257 </test>
156 <test> 258 <test>
157 <param name="input1" value="mtcars.txt"/> 259 <param name="input1" value="mtcars.txt"/>
158 <param name="cluster" value=""/> 260 <param name="cluster" value="no"/>
159 <output name="output1" file="result2.pdf" compare="sim_size"/> 261 <param name="image_file_format" value="png"/>
262 <output name="output1" file="result2.png" compare="sim_size"/>
263 </test>
264 <test>
265 <param name="input1" value="mtcars.txt"/>
266 <param name="zscore" value="cols"/>
267 <param name="cluster" value="yes"/>
268 <param name="cluster_cols_rows" value="row"/>
269 <param name="labels" value="rows"/>
270 <param name="type" value="three"/>
271 <param name="image_file_format" value="png"/>
272 <output name="output1" file="result3.png" compare="sim_size"/>
273 </test>
274 <test>
275 <param name="input1" value="mtcars.txt"/>
276 <param name="cluster" value="yes"/>
277 <param name="distance" value="pearson_correlation"/>
278 <param name="type" value="two"/>
279 <output name="output1" file="result1pearson.pdf" compare="sim_size"/>
160 </test> 280 </test>
161 </tests> 281 </tests>
162 <help><![CDATA[ 282 <help><![CDATA[
163 This tool employs the heatmap.2 function from the R gplots package and will generate a heatmap of your data. If clustering is enabled, the heatmap uses the Euclidean distance method and the Complete hierarchical clustering method by default. 283 This tool employs the heatmap.2 function from the R gplots package and will generate a heatmap of your data. If clustering is enabled, the heatmap uses the Euclidean distance method and the Complete hierarchical clustering method by default.
164 284