|
11
|
1 ---
|
|
|
2 title: 'Per sequence GC content'
|
|
|
3 output:
|
|
|
4 html_document:
|
|
|
5 number_sections: true
|
|
|
6 toc: true
|
|
|
7 theme: cosmo
|
|
|
8 highlight: tango
|
|
|
9 ---
|
|
|
10
|
|
|
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
|
|
|
12 knitr::opts_chunk$set(
|
|
|
13 echo = ECHO,
|
|
|
14 error = TRUE
|
|
|
15 )
|
|
|
16 ```
|
|
|
17
|
|
|
18 ### Per sequence GC content
|
|
|
19
|
|
|
20 ```{r 'Per sequence GC content', fig.width=10}
|
|
|
21 ## reads 1
|
|
|
22 psGCc_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per sequence GC content')
|
|
|
23 psGCc_1$trim = 'before'
|
|
|
24
|
|
|
25 ## reads 2
|
|
|
26 psGCc_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per sequence GC content')
|
|
|
27 psGCc_2$trim = 'after'
|
|
|
28
|
|
|
29 comb_psGCc = rbind(psGCc_1, psGCc_2)
|
|
|
30 comb_psGCc$trim = factor(levels = c('before', 'after'), comb_psGCc$trim)
|
|
|
31
|
|
|
32 p = ggplot(data = comb_psGCc, aes(x = X.GC.Content, y = Count)) +
|
|
|
33 geom_line(color = 'red') +
|
|
|
34 facet_grid(. ~ trim) +
|
|
|
35 xlab('Mean Sequence Qaulity (Phred Score)') +
|
|
|
36 ylab('')
|
|
|
37 ggplotly(p)
|
|
|
38 ``` |
