Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site

comparison 05_per_base_sequence_content.Rmd @ 11:507eec497730 draft

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update fastqc site
author mingchen0919
date Tue, 07 Nov 2017 16:52:24 -0500
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10:600c39b11913 11:507eec497730
1 ---
2 title: 'Per base sequence 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$set(
13 echo = ECHO,
14 error = TRUE
15 )
16 ```
17
18 ### Per base sequence content
19
20 ```{r 'Per base sequence content', fig.width=10}
21 ## reads 1
22 pbsc_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per base sequence content')
23 pbsc_1$id = 1:length(pbsc_1$X.Base)
24
25 melt_pbsc_1 = melt(pbsc_1, id=c('X.Base', 'id'))
26 melt_pbsc_1$trim = 'before'
27
28
29 ## reads 2
30 pbsc_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per base sequence content')
31 pbsc_2$id = 1:length(pbsc_2$X.Base)
32
33 melt_pbsc_2 = melt(pbsc_2, id=c('X.Base', 'id'))
34 melt_pbsc_2$trim = 'after'
35
36 comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2)
37 comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim)
38
39 p = ggplot(data = comb_pbsc, aes(x = id, y = value, color = variable)) +
40 geom_line() +
41 facet_grid(. ~ trim) +
42 xlim(min(comb_pbsc$id), max(comb_pbsc$id)) +
43 ylim(0, 100) +
44 xlab('Position in read (bp)') +
45 ylab('')
46 ggplotly(p)
47 ```