added lables to plots

mv-lab · Nov 18, 2019 · 06445ca · 06445ca
1 parent 715b738
commit 06445ca
Show file tree

Hide file tree

Showing 3 changed files with 20 additions and 2 deletions.
diff --git a/rules/denovo.rules.smk b/rules/denovo.rules.smk
@@ -32,15 +32,15 @@ rule pca_mash:
     output:
         "output/plots/denovo/mash/pca.pdf", 
     script:
-        "../scripts/pca.R"
+        "../scripts/pca_mash.R"
 
 rule pca_kwip:
     input:
         rules.kwip.input,
     output:
         "output/plots/denovo/kwip/pca.pdf",
     script:
-        "../scripts/pca.R"
+        "../scripts/pca_kwip.R"
 
 
 

diff --git a/scripts/pca.R → scripts/pca_kwip.R b/scripts/pca.R → scripts/pca_kwip.R
@@ -5,8 +5,11 @@ print (snakemake@output[[1]])
 
 y0<-read.delim(snakemake@input[[1]], header=T)
 data<-as.matrix(y0[, -1])
+labels<-colnames(data)
 pca <- prcomp(data, scale=F)
 print ('PCA done!')
 plot3d(pca$x[,c(1,2,3)], size=10)
+text3d(pca$x[,c(1,2,3)], text=labels)
 rgl.postscript(snakemake@output[[1]],"pdf")
+rgl.postscript(snakemake@output[[1]],"svg")
 
diff --git a/scripts/pca_mash.R b/scripts/pca_mash.R
@@ -0,0 +1,15 @@
+library(rgl)
+
+print (snakemake@input[[1]])
+print (snakemake@output[[1]])
+
+y0<-read.delim(snakemake@input[[1]], header=T)
+data<-as.matrix(y0[, -1])
+labels<-as.data.frame(do.call(rbind, strsplit(colnames(data), "[.]")))$V4
+pca <- prcomp(data, scale=F)
+print ('PCA done!')
+plot3d(pca$x[,c(1,2,3)], size=10)
+text3d(pca$x[,c(1,2,3)], text=labels)
+rgl.postscript(snakemake@output[[1]],"pdf")
+rgl.postscript(snakemake@output[[1]],"svg")
+