Mercurial > repos > artbio > gsc_high_dimensions_visualisation
changeset 2:7e7a2a4cfce2 draft
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(-) [+] |
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--- 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 @@ +id factor +1001000173.G8 a +1001000173.B4 a +1001000173.A2 a +1001000173.E2 a +1001000173.F6 a +1001000173.B12 a +1001000173.H1 a +1001000173.E4 a +1001000173.C2 a +1001000173.F4 a +1001000173.E10 a +1001000173.E6 a +1001000173.C4 a +1001000173.B10 a +1001000173.A7 a +1001000173.B8 a +1001000173.F9 a +1001000173.G6 a +1001000173.A9 a +1001000173.D2 a +1001000173.F2 a +1001000173.H9 a +1001000173.G1 a +1001000173.B3 a +1001000173.D7 a +1001000173.A12 a +1001000173.C1 a +1001000173.H7 a +1001000173.H5 a +1001000173.G2 a +1001000173.A3 a +1001000173.D3 a +1001000173.E1 a +1001000173.G12 a +1001000173.C10 a +1001000173.C3 a +1001000173.A5 a +1001000173.G4 a +1001000173.B11 a +1001000173.G9 a +1001000173.F1 a +1001000173.D8 a +1001000173.E12 a +1001000173.F11 a +1001000173.E5 a +1001000173.G10 a +1001000173.B9 a +1001000173.C7 a +1001000173.B2 a +1001000173.H4 a 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