Mercurial > repos > mingchen0919 > aurora_fastqc_site
annotate 09_sequence_duplication_levels.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 |
|---|---|
| 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
diff
changeset
|
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 | |
| 10 | |
| 3 | 11 ### Sequence Duplication Levels |
| 1 | 12 |
| 13 ```{r 'Sequence Duplication Levels', fig.width=10} | |
| 14 ## reads 1 | |
| 15 sdl_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#') | |
| 16 names(sdl_1) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total') | |
| 17 sdl_1$id = 1:length(sdl_1$Duplication_Level) | |
| 18 | |
| 19 melt_sdl_1 = melt(sdl_1, id=c('Duplication_Level', 'id')) | |
| 20 melt_sdl_1$trim = 'before' | |
| 21 | |
| 22 | |
| 23 ## reads 2 | |
| 24 sdl_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#') | |
| 25 names(sdl_2) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total') | |
| 26 sdl_2$id = 1:length(sdl_2$Duplication_Level) | |
| 27 | |
| 28 melt_sdl_2 = melt(sdl_2, id=c('Duplication_Level', 'id')) | |
| 29 melt_sdl_2$trim = 'after' | |
| 30 | |
| 31 comb_sdl = rbind(melt_sdl_1, melt_sdl_2) | |
| 32 comb_sdl$trim = factor(levels = c('before', 'after'), comb_sdl$trim) | |
| 33 | |
| 3 | 34 p = ggplot(data = comb_sdl) + |
| 35 geom_line(mapping = aes(x = id, y = value, color = variable)) + | |
| 1 | 36 scale_x_continuous(breaks = sdl_2$id, labels = sdl_2$Duplication_Level) + |
| 37 facet_grid(. ~ trim) + | |
| 38 xlab('Sequence Duplication Level') + | |
| 39 ylab('') + | |
| 3 | 40 scale_color_discrete(name = '') + |
| 41 theme(axis.text.x = element_text(size = 5), | |
| 42 panel.background = element_rect(fill = NA), | |
| 43 axis.line = element_line()) | |
| 44 p | |
| 45 ``` |