added clustering and PCA plot and scree plots

workflow/rules/computeDmrs.smk

@@ -19,6 +19,9 @@ rule compute_methylkit:
 		coverageStatsPdf=outdir+"methylkit_results/{id}-{context}/{id}-{context}-coverage-stats.pdf",
 		correlationTxt=outdir+"methylkit_results/{id}-{context}/{id}-{context}-correlation-stats.txt",
 		correlationPdf=outdir+"methylkit_results/{id}-{context}/{id}-{context}-correlation-stats.pdf",
+		clustersPdf=outdir+"methylkit_results/{id}-{context}/{id}-{context}-clusters.pdf",
+		pcaScreePdf=outdir+"methylkit_results/{id}-{context}/{id}-{context}-PCA-screeplot.pdf",
+		pcaPdf=outdir+"methylkit_results/{id}-{context}/{id}-{context}-PCA.pdf",
 
 	log:
 		outdir+"methylkit_results/{id}-{context}/{id}-{context}-log.out"

workflow/scripts/methylkit.R

@@ -84,3 +84,17 @@ close(fileTxt)
 pdf(snakemake@output[["correlationPdf"]])
 getCorrelation(meth,plot=TRUE)
 dev.off()
+
+
+pdf(snakemake@output[["clustersPdf"]])
+clusterSamples(meth, dist="correlation", method="ward.D2", plot=TRUE)
+dev.off()
+### PCA ###
+pdf(snakemake@output[["pcaScreePdf"]])
+PCASamples(meth, screeplot=TRUE)
+dev.off()
+
+
+pdf(snakemake@output[["pcaPdf"]])
+PCASamples(meth)
+dev.off()