Mercurial > repos > artbio > gsc_high_dimensions_visualisation

changeset 2:7e7a2a4cfce2 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
author artbio
date Tue, 25 Jun 2019 16:20:27 -0400
parents c756ab726a85
children 8e44c9e18a56
files high_dim_visu.R high_dim_visu.xml test-data/2-lev_factor.tsv test-data/pca.nolabels.2-lev-factor.pdf
diffstat 4 files changed, 1052 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/high_dim_visu.R	Mon Jun 24 19:16:53 2019 -0400
+++ b/high_dim_visu.R	Tue Jun 25 16:20:27 2019 -0400
@@ -229,11 +229,16 @@
   contrasting_factor <- contrasting_factor[colnames(data),]
   colnames(contrasting_factor) <- c("id","factor")
   contrasting_factor$factor <- as.factor(contrasting_factor$factor)
+  if(nlevels(contrasting_factor$factor) == 2){
+    colors_labels <- c("#E41A1C", "#377EB8")
+  } else {
+    colors_labels <- brewer.pal(nlevels(contrasting_factor$factor), name = 'Paired')
+  }
   factorColors <-
     with(contrasting_factor,
-         data.frame(factor = levels(factor),
-                    data.frame(factor = levels(factor),
-                               color = I(brewer.pal(nlevels(factor), name = 'Paired'))))
+         data.frame(factor = levels(contrasting_factor$factor),
+                    color = I(colors_labels)
+         )
     )
   factor_cols <- factorColors$color[match(contrasting_factor$factor,
                                           factorColors$factor)]
--- a/high_dim_visu.xml	Mon Jun 24 19:16:53 2019 -0400
+++ b/high_dim_visu.xml	Tue Jun 25 16:20:27 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.1">
+<tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.2">
     <description>from highly dimensional expression data</description>
     <requirements>
         <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
@@ -206,6 +206,15 @@
             <param name="factor" value="factor.tsv" ftype="txt"/>
             <output name="pdf_out" file="pca.nolabels.factors.pdf" ftype="pdf"/>
         </test>
+        <!-- test two-level factor contrasting on PCA -->
+        <test>
+            <param name="input" value="cpm_input.tsv" ftype="txt"/>
+            <param name="labels" value="no" />
+            <param name="visu_choice" value="PCA" />
+            <param name="factor_choice" value="Yes" />
+            <param name="factor" value="2-lev_factor.tsv" ftype="txt"/>
+            <output name="pdf_out" file="pca.nolabels.2-lev-factor.pdf" ftype="pdf"/>
+        </test>
         <test>
             <param name="input" value="cpm_input.tsv" ftype="txt"/>
             <param name="labels" value="no" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-lev_factor.tsv	Tue Jun 25 16:20:27 2019 -0400
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