changeset 2:7e7a2a4cfce2 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671

--- 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
@@ -0,0 +1,1034 @@
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[phone].F12	b
[phone].B4	b
[phone].E1	b
[phone].F2	b
[phone].B10	b
[phone].E3	b
[phone].D11	b
[phone].D8	b
[phone].H4	b
[phone].G10	b
[phone].F4	b
[phone].G12	b
[phone].B5	b
[phone].C2	b
[phone].F6	b
[phone].A10	b
[phone].E10	b
[phone].B8	b
[phone].H10	b
[phone].A12	b
[phone].A5	b
[phone].C9	b
[phone].G2	b
[phone].F10	b
[phone].D5	b
[phone].G9	b
[phone].B3	b
[phone].B1	b
[phone].G10	b
[phone].G3	b
[phone].D7	b
[phone].H11	b
[phone].C2	b
[phone].G5	b
[phone].A11	b
[phone].G8	b
[phone].H2	b
[phone].H9	b
[phone].C8	b
[phone].E9	b
[phone].A2	b
[phone].B2	b
[phone].D4	b
[phone].G4	b
[phone].A1	b
[phone].B9	b
[phone].B7	b
[phone].D6	b
[phone].G3	b
[phone].F10	b
[phone].G7	b
[phone].H5	b
[phone].H4	b
[phone].F1	b
[phone].G4	b
[phone].C3	b
[phone].H4	b
[phone].F2	b
[phone].C2	b
[phone].B8	b
[phone].F5	b
[phone].H7	b
[phone].F2	b
[phone].E2	b
[phone].A2	b
[phone].B2	b
[phone].G7	b
[phone].G1	b
[phone].F6	b
[phone].A3	b
[phone].C11	b
[phone].F7	b
[phone].B4	b
[phone].B1	b
[phone].G2	b
[phone].F5	b
[phone].B12	b
[phone].B2	b
[phone].G6	b
[phone].A6	b
[phone].H3	b
[phone].B1	b
[phone].C6	b
[phone].G9	b
[phone].G12	b
[phone].A12	b
[phone].B5	b
[phone].F6	b
[phone].B1	b
[phone].A9	b
[phone].G2	b
[phone].A11	b
[phone].F7	b
[phone].E1	b
[phone].B4	b
[phone].D8	b
[phone].G6	b
[phone].H4	b
[phone].A7	b
[phone].D9	b
[phone].C2	b
[phone].B4	b
[phone].C2	b
[phone].G1	b
[phone].D5	b
[phone].F10	b
[phone].F8	b
[phone].D12	b
[phone].F11	b
[phone].D12	b
[phone].C12	b
[phone].H5	b
[phone].A12	b
[phone].G1	b
[phone].H11	b
[phone].H1	b
[phone].F12	b
[phone].B9	b
[phone].G10	b
[phone].F7	b
[phone].C9	b
[phone].G11	b
[phone].G9	b
[phone].H10	b
[phone].E8	b
[phone].E4	b
[phone].D7	b
[phone].F6	b
[phone].G3	b
[phone].A12	b
[phone].F4	b
[phone].G6	b
[phone].B7	b
[phone].F2	b
[phone].C9	b
[phone].A4	b
[phone].C4	b
[phone].A10	b
[phone].G10	b
[phone].C2	b
[phone].H2	b
[phone].B10	b
[phone].F3	b
[phone].E2	b
[phone].D7	b
[phone].C10	b
[phone].B6	b
[phone].F11	b
[phone].A6	b
[phone].C1	b
[phone].E7	b
[phone].D2	b
[phone].H1	b
[phone].G12	b
[phone].G11	b
[phone].D5	b
[phone].E8	b
[phone].H4	b
[phone].G1	b
[phone].G9	b
[phone].B2	b
[phone].F2	b
[phone].A5	b
[phone].D5	b
[phone].A10	b
[phone].H9	b
[phone].B4	b
[phone].E2	b
[phone].E9	b
[phone].A7	b
[phone].C11	b
[phone].A1	b
[phone].E6	b
[phone].B6	b
[phone].G5	b
[phone].E4	b
[phone].B12	b
[phone].D12	b
[phone].B10	b
[phone].G7	b
[phone].B1	b
[phone].F7	b
[phone].D6	b
[phone].B5	b
[phone].H11	b
[phone].D4	b
[phone].G3	b
[phone].A2	b
[phone].C6	b
[phone].F1	b
[phone].B11	b
[phone].B9	b
[phone].C12	b
[phone].G4	b
[phone].F11	b
[phone].E12	b
[phone].E1	b
[phone].A9	b
[phone].A4	b
[phone].C10	b
[phone].F12	b
[phone].E10	b
[phone].C8	b
[phone].E5	b
[phone].E3	b
[phone].B3	b
[phone].D9	b
[phone].G10	b
[phone].B8	b
[phone].G5	b
[phone].D6	b
[phone].F6	b
[phone].C6	b
[phone].F1	b
[phone].H2	b
[phone].B2	b
[phone].G2	b
[phone].A2	b
[phone].H4	b
[phone].H5	b
[phone].C3	b
[phone].D5	b
[phone].C5	b
[phone].F5	b
[phone].B5	b
[phone].E6	b
[phone].E4	b
[phone].H3	b
[phone].E2	b
[phone].G1	b
[phone].B1	b
[phone].A3	b

Binary file test-data/pca.nolabels.2-lev-factor.pdf has changed