|
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
|
|
3
|
13 ### Adapter Content
|
|
1
|
14
|
|
|
15 ```{r 'Adapter Content', fig.width=10}
|
|
|
16 ## reads 1
|
|
|
17 ac_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Adapter Content')
|
|
|
18 ac_1$id = 1:length(ac_1$X.Position)
|
|
|
19
|
|
|
20 melt_ac_1 = melt(ac_1, id=c('X.Position', 'id'))
|
|
|
21 melt_ac_1$trim = 'before'
|
|
|
22
|
|
|
23 ## reads 2
|
|
|
24 ac_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Adapter Content')
|
|
|
25 ac_2$id = 1:length(ac_2$X.Position)
|
|
|
26
|
|
|
27 melt_ac_2 = melt(ac_2, id=c('X.Position', 'id'))
|
|
|
28 melt_ac_2$trim = 'after'
|
|
|
29
|
|
|
30 comb_ac = rbind(melt_ac_1, melt_ac_2)
|
|
|
31 comb_ac$trim = factor(levels = c('before', 'after'), comb_ac$trim)
|
|
|
32
|
|
|
33 p = ggplot(data = comb_ac, aes(x = id, y = value, color = variable)) +
|
|
|
34 geom_line() +
|
|
|
35 facet_grid(. ~ trim) +
|
|
|
36 xlim(min(comb_ac$id), max(comb_ac$id)) +
|
|
|
37 ylim(0, 1) +
|
|
|
38 xlab('Position in read (bp)') +
|
|
3
|
39 ylab('') +
|
|
|
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())
|
|
1
|
44 ggplotly(p)
|
|
3
|
45 ```
|
