Mercurial > repos > mingchen0919 > rmarkdown_deseq2
annotate DESeq_visualization.Rmd @ 3:15a5fb1a2ac8 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 11:45:42 -0400 |
parents | a0d37b034e45 |
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rev | line source |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
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1 --- |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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2 title: 'DESeq2: Visualization' |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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3 output: |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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4 html_document: |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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5 number_sections: true |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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6 toc: true |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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7 theme: cosmo |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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8 highlight: tango |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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9 --- |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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10 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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12 knitr::opts_chunk$set( |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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13 echo = ECHO |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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14 ) |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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15 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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16 library(stringi) |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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17 library(DESeq2) |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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18 library(pheatmap) |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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19 # library(PoiClaClu) |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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20 library(RColorBrewer) |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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21 ``` |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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22 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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23 # Import workspace |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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24 |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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25 ```{r eval=TRUE} |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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26 fcp = file.copy("DESEQ_WORKSPACE", "deseq.RData") |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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27 load("deseq.RData") |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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28 ``` |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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29 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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30 # Visualization |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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31 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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32 ## Heatmaps of sample-to-sample distances {.tabset} |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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33 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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34 ### rlog-transformed values |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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35 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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36 ```{r} |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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37 sampleDistMatrix <- as.matrix( sampleDists ) |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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38 colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255) |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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39 pheatmap(sampleDistMatrix, |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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40 # clustering_distance_rows = sampleDists, |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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41 clustering_distance_cols = sampleDists, |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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42 col = colors) |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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43 ``` |
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44 |
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45 ### Poisson Distance |
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46 |
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47 ```{r eval=FALSE} |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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48 count_t = t(counts(dds)) |
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49 rownames(count_t) = colnames(counts(dds)) |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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50 poisd <- PoissonDistance(count_t) |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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51 samplePoisDistMatrix <- as.matrix( poisd$dd ) |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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52 rownames(samplePoisDistMatrix) = rownames(count_t) |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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53 colnames(samplePoisDistMatrix) = rownames(count_t) |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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54 pheatmap(samplePoisDistMatrix, |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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55 # clustering_distance_rows = poisd$dd, |
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56 clustering_distance_cols = poisd$dd, |
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57 col = colors) |
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58 ``` |
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59 |
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60 |
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61 ## PCA plots {.tabset} |
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62 |
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63 ### Using `plotPCA()` function |
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64 |
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65 ```{r} |
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66 # interest groups |
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67 col_index = as.numeric(strsplit("INTGROUPS_PCA", ',')[[1]]) |
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68 intgroup_pca = colnames(sample_table)[col_index] |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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69 ``` |
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70 |
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71 ```{r} |
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72 plotPCA(rld, intgroup = intgroup_pca) |
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73 ``` |
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74 |
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75 |
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76 ### Using *ggplot2* |
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77 |
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78 ```{r} |
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79 pcaData <- plotPCA(rld, intgroup = intgroup_pca, returnData = TRUE) |
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80 percentVar <- round(100 * attr(pcaData, "percentVar")) |
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81 ggplot(pcaData, aes(x = PC1, y = PC2, color = time)) + |
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82 geom_point(size =3) + |
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83 xlab(paste0("PC1: ", percentVar[1], "% variance")) + |
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84 ylab(paste0("PC2: ", percentVar[2], "% variance")) + |
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85 coord_fixed() |
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86 ``` |
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87 |
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88 ### PCA data table |
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89 |
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90 ```{r} |
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91 knitr::kable(pcaData) |
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92 ``` |
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93 |
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94 |
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95 ## MDS plots {.tabset} |
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96 |
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97 ### Using rlog-transformed values |
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98 |
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99 ```{r} |
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100 mds <- as.data.frame(colData(rld)) %>% |
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101 cbind(cmdscale(sampleDistMatrix)) |
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102 mds |
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103 ggplot(mds, aes(x = `1`, y = `2`, col = time)) + |
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104 geom_point(size = 3) + coord_fixed() |
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105 ``` |
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106 |
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107 ### Using the *Poisson Distance* |
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108 |
2
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109 ```{r eval=FALSE} |
0
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110 mdsPois <- as.data.frame(colData(dds)) %>% |
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111 cbind(cmdscale(samplePoisDistMatrix)) |
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112 ggplot(mdsPois, aes(x = `1`, y = `2`, col = time)) + |
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113 geom_point(size = 3) + coord_fixed() |
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114 ``` |