Mercurial > repos > iuc > ggplot2_heatmap2
changeset 5:3b37b1b1c3a7 draft
"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 |
| files | heatmap2.xml test-data/result1pearson.pdf test-data/result2.pdf test-data/result2.png test-data/result3.png |
| diffstat | 5 files changed, 187 insertions(+), 67 deletions(-) [+] |
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--- a/heatmap2.xml Mon Feb 11 17:32:28 2019 -0500 +++ b/heatmap2.xml Tue Apr 12 15:53:40 2022 +0000 @@ -1,10 +1,10 @@ <tool id="ggplot2_heatmap2" name="heatmap2" version="@VERSION@"> <macros> - <token name="@VERSION@">3.0.1</token> + <token name="@VERSION@">3.1.1</token> </macros> <requirements> <requirement type="package" version="@VERSION@">r-gplots</requirement> - <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> + <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ cat '$script' && @@ -39,63 +39,91 @@ linput <- log10(mat_input+1) #end if -#if $colorscheme == "whrd" - colorscale = colfunc <- colorRampPalette(c("white", "red")) -#elif $colorscheme == "whblu" - colorscale = colfunc <- colorRampPalette(c("white", "blue")) -#elif $colorscheme == "blwhre" - colorscale = colfunc <- colorRampPalette(c("blue","white", "red")) +#if $zscore_cond.zscore == "rows": + linput <- t(apply(linput, 1, scale)) + colnames(linput) <- colnames(input) + rownames(linput) <- input[,1] + scale <- "none" +#elif $zscore_cond.zscore == "cols": + linput <- apply(linput, 2, scale) + rownames(linput) <- input[,1] + scale <- "none" +#elif $zscore_cond.zscore == "none": + scale <- "$zscore_cond.scale" #end if -#if $labels== "both" - rlabs = NULL - clabs = NULL -#elif $labels== "rows" - rlabs = NULL - clabs = FALSE -#elif $labels== "columns" - rlabs = FALSE - clabs = NULL -#elif $labels== "none" - rlabs = FALSE - clabs = FALSE +srtCol <- 45 +#if $labels == "both" + rlabs <- NULL + clabs <- NULL +#elif $labels == "rows" + rlabs <- NULL + clabs <- FALSE + srtCol <- NULL +#elif $labels == "columns" + rlabs <- FALSE + clabs <- NULL +#elif $labels == "none" + rlabs <- FALSE + clabs <- FALSE + srtCol <- NULL #end if -pdf(file='$output1') -colorscale +#if $cluster_cond.cluster == "yes": + dendrogramtoplot <- "$cluster_cond.cluster_cols_rows" + #if $cluster_cond.cluster_cols_rows == "both" + reorder_cols <- TRUE + reorder_rows <- TRUE + #elif $cluster_cond.cluster_cols_rows == "row" + reorder_cols <- FALSE + reorder_rows <- TRUE + #elif $cluster_cond.cluster_cols_rows == "column" + reorder_cols <- TRUE + reorder_rows <- FALSE + #end if + hclust_fun <- function(x) hclust(x, method='$cluster_cond.clustering') + #if $cluster_cond.distance == 'pearson_correlation': + dist_fun <- function(x) as.dist(1 - cor(t(x))) + #elif $cluster_cond.distance == 'spearmann_correlation': + dist_fun <- function(x) as.dist(1 - cor(t(x), method="spearman")) + #else: + dist_fun <- function(x) dist(x, method='$cluster_cond.distance') + #end if +#else: + dendrogramtoplot <- "none" + reorder_cols <- FALSE + reorder_rows <- FALSE + hclust_fun <- hclust + dist_fun <- dist +#end if -#if $cluster_cond.cluster: - hclust_fun = function(x) hclust(x, method='$cluster_cond.clustering') - dist_fun = function(x) dist(x, method='$cluster_cond.distance') - #if $cluster_cond.cluster_cols_rows=="rows": - heatmap.2(linput, dendrogram="row", Colv=FALSE, Rowv=TRUE, - distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs, - col=colfunc(50), trace="none", density.info = "none", margins=c(8,8), - main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45) - #elif $cluster_cond.cluster_cols_rows=="columns": - heatmap.2(linput, dendrogram="column", Colv=TRUE, Rowv=FALSE, - distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs, - col=colfunc(50), trace="none", density.info = "none", margins=c(8,8), - main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45) - #else - heatmap.2(linput, - distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs, - col=colfunc(50), trace="none", density.info = "none", margins=c(8,8), - main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45) - #end if -#else - heatmap.2(linput, - dendrogram="none", Colv=FALSE, Rowv=FALSE, scale = '$scale', labRow = rlabs, labCol = clabs, - col=colfunc(50), trace="none", density.info = "none", margins=c(8,8), - main='$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45) +ncolors <- 50 +#if $colorchoice.type == "palettes": + colused <- brewer.pal(ncolors, "$colorchoice.name") +#elif $colorchoice.type == "two" + colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2"))(ncolors) +#elif $colorchoice.type == "three" + colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2", "$colorchoice.color3"))(ncolors) #end if +#if $image_file_format == "pdf": + pdf(file='$output1') +#else: + png(file='$output1') +#end if + +heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows, + distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs, + col=colused, trace="none", density.info = "none", margins=c(8,8), + main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=srtCol) + dev.off() ]]></configfile> </configfiles> <inputs> - <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/> + <param name="input1" type="data" format="tabular" + label="Input should have column headers - these will be the columns that are plotted and row names."/> <param name="title" type="text" format="txt" label="Plot title"/> <param name="key" type="text" format="txt" label="key title"/> <param name="transform" type="select" label="Data transformation"> @@ -105,27 +133,55 @@ <option value="log10">Log10(value) transform my data</option> <option value="log10plus1">Log10(value+1) transform my data</option> </param> + <conditional name="zscore_cond"> + <param name="zscore" type="select" label="Compute z-scores prior to clustering"> + <option value="none">Do not compute z-scores</option> + <option value="rows">Compute on rows</option> + <option value="cols">Compute on columns</option> + </param> + <when value="none"> + <param name="scale" type="select" label="Scale data on the plot (after clustering)" > + <option value="none" selected="true">Do not scale my data</option> + <option value="row">Scale my data by row</option> + <option value="column">Scale my data by column</option> + </param> + </when> + <when value="rows"/> + <when value="cols"/> + </conditional> <conditional name="cluster_cond"> <param name="cluster" type="select" label="Enable data clustering"> - <option value="true">Yes</option> - <option value="">No</option> + <option value="yes">Yes</option> + <option value="no">No</option> </param> - <when value="true"> + <when value="yes"> <param name="cluster_cols_rows" type="select" label="Clustering columns and rows"> <option value="both" selected="true">Cluster rows and columns</option> - <option value="rows">Cluster rows and not columns</option> - <option value="columns">Cluster columns and not rows</option> + <option value="row">Cluster rows and not columns</option> + <option value="column">Cluster columns and not rows</option> </param> <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" > <option value="euclidean" selected="true">Euclidean</option> <option value="maximum">Maximum</option> + <option value="manhattan">Manhattan</option> + <option value="canberra">Canberra</option> + <option value="binary">Binary</option> + <option value="minkowski">Minkowski</option> + <option value="pearson_correlation">Pearson's correlation (1 - correlation coefficient)</option> + <option value="spearmann_correlation">Spearmann's correlation (1 - correlation coefficient)</option> </param> <param name="clustering" type="select" label="Clustering method" help="The method used to compute the hierarchical clustering. Default: Complete" > <option value="complete" selected="true">Complete</option> - <option value="average">Average</option> + <option value="average">Average (= UPGMA)</option> + <option value="ward.D">ward.D</option> + <option value="ward.D2">ward.D2</option> + <option value="single">single</option> + <option value="mcquitty">mcquitty (= WPGMA)</option> + <option value="median">median (= WPGMC)</option> + <option value="centroid">centroid (= UPGMC)</option> </param> </when> - <when value=""/> + <when value="no"/> </conditional> <param name="labels" type="select" label="Labeling columns and rows" > <option value="both" selected="true">Label my columns and rows</option> @@ -133,30 +189,94 @@ <option value="columns">Label columns and not rows</option> <option value="none">Do not label rows or columns</option> </param> - <param name="colorscheme" type="select" label="Coloring groups" > - <option value="whrd" selected="true">White to red</option> - <option value="whblu">White to blue</option> - <option value="blwhre">Blue to white to red</option> - </param> - <param name="scale" type="select" label="Data scaling" > - <option value="none" selected="true">Do not scale my data</option> - <option value="row">Scale my data by row</option> - <option value="column">Scale my data by column</option> + <conditional name="colorchoice"> + <param name="type" type="select" label="Type of colormap to use"> + <option value="palettes">RColorBrewer palettes</option> + <option value="two">Gradient with 2 colors</option> + <option value="three">Gradient with 3 colors</option> + </param> + <when value="palettes"> + <param name="name" type="select" label="Name of the colormap"> + <option value="BrBG">BrBG</option> + <option value="PiYG">PiYG</option> + <option value="PRGn">PRGn</option> + <option value="PuOr">PuOr</option> + <option value="RdBu">RdBu</option> + <option value="RdGy">RdGy</option> + <option value="RdYlBu">RdYlBu</option> + <option value="RdYlGn">RdYlGn</option> + <option value="Spectral">Spectral</option> + <option value="Blues">Blues</option> + <option value="BuGn">BuGn</option> + <option value="BuPu">BuPu</option> + <option value="GnBu">GnBu</option> + <option value="Greens">Greens</option> + <option value="Greys">Greys</option> + <option value="Oranges">Oranges</option> + <option value="OrRd">OrRd</option> + <option value="PuBu">PuBu</option> + <option value="PuBuGn">PuBuGn</option> + <option value="PuRd">PuRd</option> + <option value="Purples">Purples</option> + <option value="RdPu">RdPu</option> + <option value="Reds">Reds</option> + <option value="YlGn">YlGn</option> + <option value="YlGnBu">YlGnBu</option> + <option value="YlOrBr">YlOrBr</option> + <option value="YlOrRd">YlOrRd</option> + </param> + </when> + <when value="two"> + <param name="color1" type="color" value="#ffffff" label="First color" /> + <param name="color2" type="color" value="#ff0000" label="Second color" /> + </when> + <when value="three"> + <param name="color1" type="color" value="#0000ff" label="First color" /> + <param name="color2" type="color" value="#ffffff" label="Second color" /> + <param name="color3" type="color" value="#ff0000" label="Third color" /> + </when> + </conditional> + <param name="image_file_format" type="select" label="Output format"> + <option value="pdf">PDF</option> + <option value="png">PNG</option> </param> </inputs> <outputs> - <data name="output1" format="pdf"/> + <data name="output1" format="pdf"> + <change_format> + <when input="image_file_format" value="png" format="png" /> + </change_format> + </data> </outputs> <tests> <test> <param name="input1" value="mtcars.txt"/> - <param name="cluster" value="true"/> + <param name="cluster" value="yes"/> + <param name="type" value="two"/> <output name="output1" file="result1.pdf" compare="sim_size"/> </test> <test> <param name="input1" value="mtcars.txt"/> - <param name="cluster" value=""/> - <output name="output1" file="result2.pdf" compare="sim_size"/> + <param name="cluster" value="no"/> + <param name="image_file_format" value="png"/> + <output name="output1" file="result2.png" compare="sim_size"/> + </test> + <test> + <param name="input1" value="mtcars.txt"/> + <param name="zscore" value="cols"/> + <param name="cluster" value="yes"/> + <param name="cluster_cols_rows" value="row"/> + <param name="labels" value="rows"/> + <param name="type" value="three"/> + <param name="image_file_format" value="png"/> + <output name="output1" file="result3.png" compare="sim_size"/> + </test> + <test> + <param name="input1" value="mtcars.txt"/> + <param name="cluster" value="yes"/> + <param name="distance" value="pearson_correlation"/> + <param name="type" value="two"/> + <output name="output1" file="result1pearson.pdf" compare="sim_size"/> </test> </tests> <help><![CDATA[