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