| Previous changeset 2:27e62af48a5a (2016-12-11) Next changeset 4:2fee8da6aabb (2016-12-23) |
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Commit message:
planemo upload |
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modified:
plotheatmap.xml tools/script.R |
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| diff -r 27e62af48a5a -r db5d126bf8d0 plotheatmap.xml --- a/plotheatmap.xml Sun Dec 11 19:15:22 2016 -0500 +++ b/plotheatmap.xml Thu Dec 22 18:19:53 2016 -0500 |
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| @@ -5,17 +5,51 @@ </stdio> <command> <![CDATA[ - $__tool_directory__/tools/script.R $count_matrix $stats_matrix $log_fc $log_cpm $pvalue $fdr > $rscript_log 2> $rerror_log + $__tool_directory__/tools/script.R $main.count_matrix $main.stats_matrix $main.log_fc $main.log_cpm $main.pvalue $main.fdr $heatmap.cluster_row $heatmap.cluster_col $heatmap.hclust_method $plotparm.col_marg $plotparm.row_marg $plotparm.pdf_width $plotparm.pdf_height > $rscript_log 2> $rerror_log ]]> </command> <inputs> - <param name="count_matrix" type="data" format="data" label=""/> - <param name="stats_matrix" type="data" format="data" label=""/> - <param name="log_fc" type="float" value="0.5" label=""/> - <param name="log_cpm" type="float" value="0.5" label=""/> - <param name="pvalue" type="float" value="0.5" label=""/> - <param name="fdr" type="float" value="0.5" label=""/> + <section name="main" title="Main parameters" expanded="True"> + <param name="count_matrix" type="data" format="data" label=""/> + <param name="stats_matrix" type="data" format="data" label=""/> + <param name="log_fc" type="float" value="0.5" label=""/> + <param name="log_cpm" type="float" value="0.5" label=""/> + <param name="pvalue" type="float" value="0.5" label=""/> + <param name="fdr" type="float" value="0.5" label=""/> + </section> + + <section name="heatmap" title="Heatmap parameters"> + <param name="cluster_row" type="select" label="Determines if the row dendrogram should be reordered"> + <option value="No" >No </option> + <option value="Yes" selected="true" >Yes </option> + </param> + <param name="cluster_col" type="select" label="Determines if the column dendrogram should be reordered"> + <option value="No" selected="true">No </option> + <option value="Yes" >Yes </option> + </param> + + <param name="hclust_method" type="select" label="Hierarchical clustering method"> + <option value="ward.D" >ward.D </option> + <option value="ward.D2" >ward.D2 </option> + <option value="single" >single </option> + <option value="complete" >complete </option> + <option value="average" selected="true">average </option> + <option value="mcquitty" >mcquitty </option> + <option value="median" >median </option> + <option value="centroid" >centroid </option> + </param> + </section> + + + <section name="plotparm" title="Plot parameters"> + <param name="col_marg" type="float" value="7" label="Margins or column names"/> + <param name="row_marg" type="float" value="8" label="Margins or row names"/> + <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches" /> + <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches" /> + </section> + + </inputs> <outputs> @@ -43,6 +77,7 @@ </tests> <help> <![CDATA[ + ]]> </help> <citations> |
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| diff -r 27e62af48a5a -r db5d126bf8d0 tools/script.R --- a/tools/script.R Sun Dec 11 19:15:22 2016 -0500 +++ b/tools/script.R Thu Dec 22 18:19:53 2016 -0500 |
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| @@ -8,6 +8,29 @@ pValue = args[5] fdr = args[6] +clusterRow = args[7] +clusterCol = args[8] +hclustMethod = args[9] + +mgColumnNm = as.numeric(args[10]) +mgRowNm = as.numeric(args[11]) + +pdfWidth = as.numeric(args[12]) +pdfHeight = as.numeric(args[13]) + + +if(clusterRow == "Yes"){ + clusterRow = TRUE +} else { + clusterRow = NA +} + +if(clusterCol == "Yes"){ + clusterCol = TRUE +} else { + clusterCol = NA +} + require(preprocessCore) require(gplots) @@ -49,19 +72,19 @@ rownames(countDataNormLog) = rownames(countData) #svg("heatmap.svg", width = 3+length(names), height = 1/2*length(wh)) -pdf("heatmap.pdf") +pdf("heatmap.pdf", width = pdfWidth, height = pdfHeight) heatmap.2( countDataNormLog[wh, ], density.info=c("none"), - hclustfun = function(x) hclust(x, method = "average"), + hclustfun = function(x) hclust(x, method = hclustMethod), distfun = function(x) as.dist(1-cor(t(x))), col = bluered(50), - scale = 'row', - trace = "none", #lwid = c(1, length(names)), lhei = c(1,1/3*length(wh)), -# Rowv=NA, - Colv = NA, - margins = c(7, 8) + scale = "row", + trace = "none", + Rowv = clusterRow, + Colv = clusterCol, + margins = c(mgColumnNm, mgRowNm) ) dev.off() |