Mercurial > repos > mingchen0919 > aurora_fastqc_site
comparison 07_per_base_n_content.Rmd @ 0:b7c115edd970 draft
planemo upload
author | mingchen0919 |
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date | Tue, 27 Feb 2018 10:37:12 -0500 |
parents | |
children | c64267b9f754 |
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-1:000000000000 | 0:b7c115edd970 |
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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 # Per base N content | |
14 | |
15 ```{r 'Per base N content', fig.width=10} | |
16 ## reads 1 | |
17 pbNc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base N content') | |
18 pbNc_1$id = 1:length(pbNc_1$X.Base) | |
19 pbNc_1$trim = 'before' | |
20 | |
21 ## reads 2 | |
22 pbNc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base N content') | |
23 pbNc_2$id = 1:length(pbNc_2$X.Base) | |
24 pbNc_2$trim = 'after' | |
25 | |
26 comb_pbNc = rbind(pbNc_1, pbNc_2) | |
27 comb_pbNc$trim = factor(levels = c('before', 'after'), comb_pbNc$trim) | |
28 | |
29 p = ggplot(data = comb_pbNc, aes(x = id, y = N.Count)) + | |
30 geom_line(color = 'red') + | |
31 scale_x_continuous(breaks = pbNc_2$id, labels = pbNc_2$X.Base) + | |
32 facet_grid(. ~ trim) + | |
33 ylim(0, 1) + | |
34 xlab('N-Count') + | |
35 ylab('') + | |
36 theme(axis.text.x = element_text(angle=45)) | |
37 ggplotly(p) | |
38 ``` |