Mercurial > repos > mingchen0919 > aurora_fastqc_site
annotate 05_per_base_sequence_content.Rmd @ 10:5286f3b1c9c2 draft default tip
planemo upload commit 363ef0a73d874c67326a67f51a78328906951248-dirty
| author | mingchen0919 |
|---|---|
| date | Fri, 30 Nov 2018 22:15:50 -0500 |
| parents | 94762f1cb779 |
| children |
| rev | line source |
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| 1 | 1 --- |
| 2 output: html_document | |
| 3 --- | |
| 4 | |
| 5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
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94762f1cb779
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
mingchen0919
parents:
3
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changeset
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6 knitr::opts_knit$set(progress = FALSE) |
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94762f1cb779
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
mingchen0919
parents:
3
diff
changeset
|
7 knitr::opts_chunk$set(error = TRUE, echo = FALSE) |
| 1 | 8 ``` |
| 9 | |
| 3 | 10 ### Per base sequence content |
| 1 | 11 |
| 12 ```{r 'Per base sequence content', fig.width=10} | |
| 13 ## reads 1 | |
| 14 pbsc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence content') | |
| 15 pbsc_1$id = 1:length(pbsc_1$X.Base) | |
| 16 | |
| 17 melt_pbsc_1 = melt(pbsc_1, id=c('X.Base', 'id')) | |
| 18 melt_pbsc_1$trim = 'before' | |
| 19 | |
| 20 | |
| 21 ## reads 2 | |
| 22 pbsc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence content') | |
| 23 pbsc_2$id = 1:length(pbsc_2$X.Base) | |
| 24 | |
| 25 melt_pbsc_2 = melt(pbsc_2, id=c('X.Base', 'id')) | |
| 26 melt_pbsc_2$trim = 'after' | |
| 27 | |
| 28 comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2) | |
| 29 comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim) | |
| 30 | |
| 3 | 31 p = ggplot(data = comb_pbsc) + |
| 32 geom_line(mapping = aes(x = id, y = value, color = variable)) + | |
| 1 | 33 facet_grid(. ~ trim) + |
| 34 xlim(min(comb_pbsc$id), max(comb_pbsc$id)) + | |
| 35 ylim(0, 100) + | |
| 36 xlab('Position in read (bp)') + | |
| 3 | 37 ylab('') + |
| 38 scale_color_discrete(name = '') + | |
| 39 theme_classic() | |
| 1 | 40 ggplotly(p) |
| 3 | 41 ``` |