Mercurial > repos > mingchen0919 > aurora_deseq2_site
comparison 03_count_matrix_heatmap.Rmd @ 1:32210899a3dd draft
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
| author | mingchen0919 |
|---|---|
| date | Sun, 30 Dec 2018 12:45:56 -0500 |
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| 0:6f94b4b9de44 | 1:32210899a3dd |
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| 1 --- | |
| 2 title: 'Heatmap of count matrix' | |
| 3 output: | |
| 4 html_document: | |
| 5 highlight: pygments | |
| 6 --- | |
| 7 | |
| 8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
| 9 knitr::opts_chunk$set(error = TRUE, echo = FALSE) | |
| 10 ``` | |
| 11 | |
| 12 | |
| 13 ```{r} | |
| 14 ntd <- normTransform(dds) | |
| 15 select <- order(rowMeans(counts(dds,normalized=TRUE)), | |
| 16 decreasing=TRUE)[1:20] | |
| 17 df <- as.data.frame(colData(dds)[, -ncol(colData(dds))]) | |
| 18 pheatmap(assay(ntd)[select,], annotation_col=df) | |
| 19 ``` |