diff 03_count_matrix_heatmap.Rmd @ 1:32210899a3dd draft

planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/03_count_matrix_heatmap.Rmd	Sun Dec 30 12:45:56 2018 -0500
@@ -0,0 +1,19 @@
+---
+title: 'Heatmap of count matrix'
+output:
+    html_document:
+      highlight: pygments
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(error = TRUE, echo = FALSE)
+```
+
+
+```{r}
+ntd <- normTransform(dds)
+select <- order(rowMeans(counts(dds,normalized=TRUE)),
+                decreasing=TRUE)[1:20]
+df <- as.data.frame(colData(dds)[, -ncol(colData(dds))])
+pheatmap(assay(ntd)[select,], annotation_col=df)
+```