Mercurial > repos > mingchen0919 > aurora_fastqc_site
annotate 07_per_base_n_content.Rmd @ 2:c64267b9f754 draft default tip
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author | mingchen0919 |
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date | Sun, 30 Dec 2018 12:48:14 -0500 |
parents | b7c115edd970 |
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0 | 1 --- |
2 output: html_document | |
3 --- | |
4 | |
5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
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6 knitr::opts_knit$set(progress = FALSE) |
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7 knitr::opts_chunk$set(error = TRUE, echo = FALSE) |
0 | 8 ``` |
9 | |
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10 ### Per base N content |
0 | 11 |
12 ```{r 'Per base N content', fig.width=10} | |
13 ## reads 1 | |
14 pbNc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base N content') | |
15 pbNc_1$id = 1:length(pbNc_1$X.Base) | |
16 pbNc_1$trim = 'before' | |
17 | |
18 ## reads 2 | |
19 pbNc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base N content') | |
20 pbNc_2$id = 1:length(pbNc_2$X.Base) | |
21 pbNc_2$trim = 'after' | |
22 | |
23 comb_pbNc = rbind(pbNc_1, pbNc_2) | |
24 comb_pbNc$trim = factor(levels = c('before', 'after'), comb_pbNc$trim) | |
25 | |
26 p = ggplot(data = comb_pbNc, aes(x = id, y = N.Count)) + | |
27 geom_line(color = 'red') + | |
28 scale_x_continuous(breaks = pbNc_2$id, labels = pbNc_2$X.Base) + | |
29 facet_grid(. ~ trim) + | |
30 ylim(0, 1) + | |
31 xlab('N-Count') + | |
32 ylab('') + | |
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33 theme(axis.text.x = element_text(size = 5), |
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34 axis.line = element_line(), |
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35 panel.background = element_rect(fill = NA)) |
0 | 36 ggplotly(p) |
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37 ``` |