|
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 # Per base sequence content
|
|
|
15
|
|
|
16 ```{r 'Per base sequence content', fig.width=10}
|
|
|
17 ## reads 1
|
|
|
18 pbsc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence content')
|
|
|
19 pbsc_1$id = 1:length(pbsc_1$X.Base)
|
|
|
20
|
|
|
21 melt_pbsc_1 = melt(pbsc_1, id=c('X.Base', 'id'))
|
|
|
22 melt_pbsc_1$trim = 'before'
|
|
|
23
|
|
|
24
|
|
|
25 ## reads 2
|
|
|
26 pbsc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence content')
|
|
|
27 pbsc_2$id = 1:length(pbsc_2$X.Base)
|
|
|
28
|
|
|
29 melt_pbsc_2 = melt(pbsc_2, id=c('X.Base', 'id'))
|
|
|
30 melt_pbsc_2$trim = 'after'
|
|
|
31
|
|
|
32 comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2)
|
|
|
33 comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim)
|
|
|
34
|
|
|
35 p = ggplot(data = comb_pbsc, aes(x = id, y = value, color = variable)) +
|
|
|
36 geom_line() +
|
|
|
37 facet_grid(. ~ trim) +
|
|
|
38 xlim(min(comb_pbsc$id), max(comb_pbsc$id)) +
|
|
|
39 ylim(0, 100) +
|
|
|
40 xlab('Position in read (bp)') +
|
|
|
41 ylab('')
|
|
|
42 ggplotly(p)
|
|
|
43 ``` |
