Mercurial > repos > mingchen0919 > aurora_deseq2_site
comparison DESeq_results_04.Rmd @ 0:6f94b4b9de44 draft
planemo upload
author | mingchen0919 |
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date | Tue, 27 Feb 2018 23:57:53 -0500 |
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-1:000000000000 | 0:6f94b4b9de44 |
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1 --- | |
2 output: html_document | |
3 --- | |
4 | |
5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
6 knitr::opts_chunk$set( | |
7 echo = as.logical(opt$X_e), | |
8 error = TRUE | |
9 ) | |
10 ``` | |
11 | |
12 | |
13 # Visualization {.tabset} | |
14 ## Gene clustering | |
15 | |
16 ```{r} | |
17 clustering_groups = strsplit(opt$X_M, ',')[[1]] | |
18 | |
19 topVarGenes <- head(order(rowVars(assay(rld)), decreasing = TRUE), 20) | |
20 mat <- assay(rld)[ topVarGenes, ] | |
21 mat <- mat - rowMeans(mat) | |
22 annotation_col <- as.data.frame(colData(rld)[, clustering_groups]) | |
23 colnames(annotation_col) = clustering_groups | |
24 rownames(annotation_col) = colnames(mat) | |
25 pheatmap(mat, annotation_col = annotation_col) | |
26 ``` | |
27 | |
28 ## Sample-to-sample distance | |
29 | |
30 ```{r} | |
31 sampleDistMatrix <- as.matrix( sampleDists ) | |
32 colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255) | |
33 pheatmap(sampleDistMatrix, | |
34 clustering_distance_cols = sampleDists, | |
35 col = colors) | |
36 ``` | |
37 | |
38 ## PCA plot | |
39 | |
40 ```{r} | |
41 plotPCA(rld, intgroup = clustering_groups) | |
42 ``` | |
43 | |
44 ## MDS plot {.tabset} | |
45 | |
46 ### Data table | |
47 ```{r} | |
48 mds <- as.data.frame(colData(rld)) %>% | |
49 cbind(cmdscale(sampleDistMatrix)) | |
50 knitr::kable(mds) | |
51 ``` | |
52 | |
53 ### Plot | |
54 ```{r} | |
55 ggplot(mds, aes(x = `1`, y = `2`, col = time)) + | |
56 geom_point(size = 3) + coord_fixed() | |
57 ``` |