Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site

comparison 06_per_sequence_gc_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 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 ```