Mercurial > repos > mingchen0919 > aurora_deseq2_site

annotate 03_count_matrix_heatmap.Rmd @ 1:32210899a3dd draft

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