comparison heatmap.xml @ 1:e298f66f5d8c draft default tip

"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"

0:5182b74b6435

<tool id="high_dim_heatmap" name="Plot heatmap" version="1.0.0">
    <description>with high number of rows</description>
    <requirements>
        <requirement type="package" version="3.0.1">r-gplots</requirement>
        <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
    </requirements>

library("RColorBrewer")
library("gplots")

input <- read.delim('$input1', sep='\t', header=TRUE)

mat_input <- data.matrix(input[,2:ncol(input)])
rownames(mat_input) <- input[,1]

#if $transform == "none"
    linput <- mat_input
#elif $transform == "log2"
    linput <- log2(mat_input)
#elif $transform == "log2plus1"
    linput <- log2(mat_input+1)
#elif $transform == "log10"
    linput <- log10(mat_input)
#elif $transform == "log10plus1"
    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"))
#end if

#if $labels== "both"
    rlabs = NULL
    clabs = NULL

#elif $labels== "none"
    rlabs = FALSE
    clabs = FALSE
#end if

pdf(file='$output1', paper='special', height=$height)
colorscale

#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 = $rowfontsize, srtCol=45,
            lhei=c(1, $lineheight))
    #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 = $rowfontsize, srtCol=45,
            lhei=c(1, $lineheight))
    #else
        heatmap.2(linput,
            distfun=dist_fun, hclustfun=hclust_fun, scale = '$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 = $rowfontsize, srtCol=45,
            lhei=c(1, $lineheight))
    #end if
#else
    heatmap.2(linput,
        dendrogram="none", Colv=FALSE, Rowv=FALSE, scale = '$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 = $rowfontsize, srtCol=45,
        lhei=c(1, $lineheight))
#end if

dev.off()
        ]]></configfile>
    </configfiles>

            <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>
        </param>

        <param name="height" type="float" label="tweak plot height" value="7" />
        <param name="rowfontsize" type="float" label="tweak row label size" value="0.8" />
        <param name="lineheight" type="integer" label="tweak line height" value="4" />
    </inputs>
    <outputs>
        <data name="output1" format="pdf"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="mtcars.txt"/>
            <param name="cluster" value="true"/>
            <output name="output1" file="result1.pdf"/>
        </test>
        <test>
            <param name="input1" value="mtcars.txt"/>
            <param name="cluster" value=""/>
            <output name="output1" file="result2.pdf"/>
        </test>
        <test>
            <param name="input1" value="complex_table.tsv"/>
            <param name="transform" value="log2plus1"/>
            <param name="cluster" value=""/>
            <param name="colorscheme" value="blwhre"/>
            <param name="height" value="21"/>
            <param name="rowfontsize" value="0.4"/>

1:e298f66f5d8c

<tool id="high_dim_heatmap" name="Plot heatmap" version="1.2.0">
    <description>with high number of rows</description>
    <requirements>
        <requirement type="package" version="3.0.1">r-gplots</requirement>
        <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
    </requirements>

library("RColorBrewer")
library("gplots")

input <- read.delim('$input1', sep='\t', header=TRUE)

mat_input <- data.matrix(input[, 2:ncol(input)])
rownames(mat_input) <- input[, 1]

#if $transform == "none"
    linput <- mat_input
#elif $transform == "log2"
    linput <- log2(mat_input)
#elif $transform == "log2plus1"
    linput <- log2(mat_input + 1)
#elif $transform == "log10"
    linput <- log10(mat_input)
#elif $transform == "log10plus1"
    linput <- log10(mat_input + 1)
#end if

#if $colorscheme == "whrd"
    colfunc <- colorRampPalette(c("white", "red"))
#elif $colorscheme == "whblu"
    colfunc <- colorRampPalette(c("white", "blue"))
#elif $colorscheme == "blwhre"
    colfunc <- colorRampPalette(c("blue","white", "red"))
#elif $colorscheme == "yeblu"
    colfunc <- colorRampPalette(c("lightyellow", "royalblue4"))
#end if

#if $labels== "both"
    rlabs = NULL
    clabs = NULL

#elif $labels== "none"
    rlabs = FALSE
    clabs = FALSE
#end if

pdf(file = '$output1', paper = 'special', height = $height)
par(cex.main = $title_size)

#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 = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
    #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 = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
    #else
        heatmap.2(linput,
            distfun = dist_fun, hclustfun = hclust_fun, scale = '$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 = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
    #end if
#else
    heatmap.2(linput,
        dendrogram = "none", Colv = FALSE, Rowv = FALSE, scale = '$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 = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
#end if

dev.off()
        ]]></configfile>
    </configfiles>

            <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="yeblu">Yellow 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>
        </param>

        <param name="title_size" type="float" label="tweak main title size" value="1" />
        <param name="height" type="float" label="tweak plot height" value="7" />
        <param name="rowfontsize" type="float" label="tweak row label size" value="0.8" />
        <param name="lineheight" type="integer" label="tweak line height" value="4" />
    </inputs>
    <outputs>
        <data name="output1" format="pdf"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="mtcars.txt"/>
            <param name="title" value="This is a pretty long title"/>
            <param name="cluster" value="true"/>
            <output name="output1" file="result1.pdf"/>
        </test>
        <test>
            <param name="input1" value="mtcars.txt"/>
            <param name="title" value="This is a pretty long title"/>
            <param name="cluster" value=""/>
            <output name="output1" file="result2.pdf"/>
        </test>
        <test>
            <param name="input1" value="complex_table.tsv"/>
            <param name="title" value="This is a pretty long title for a complex plot"/>
            <param name="title_size" value="0.7"/>
            <param name="transform" value="log2plus1"/>
            <param name="cluster" value=""/>
            <param name="colorscheme" value="blwhre"/>
            <param name="height" value="21"/>
            <param name="rowfontsize" value="0.4"/>