Mercurial > repos > mingchen0919 > aurora_fastqc_site
comparison 07_per_base_n_content.Rmd @ 2:c64267b9f754 draft default tip
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author | mingchen0919 |
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date | Sun, 30 Dec 2018 12:48:14 -0500 |
parents | b7c115edd970 |
children |
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1:92e3de11b9f8 | 2:c64267b9f754 |
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1 --- | 1 --- |
2 output: html_document | 2 output: html_document |
3 --- | 3 --- |
4 | 4 |
5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | 5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} |
6 knitr::opts_chunk$set( | 6 knitr::opts_knit$set(progress = FALSE) |
7 echo = as.logical(opt$X_e), | 7 knitr::opts_chunk$set(error = TRUE, echo = FALSE) |
8 error = TRUE, | |
9 eval = TRUE | |
10 ) | |
11 ``` | 8 ``` |
12 | 9 |
13 # Per base N content | 10 ### Per base N content |
14 | 11 |
15 ```{r 'Per base N content', fig.width=10} | 12 ```{r 'Per base N content', fig.width=10} |
16 ## reads 1 | 13 ## reads 1 |
17 pbNc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base N content') | 14 pbNc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base N content') |
18 pbNc_1$id = 1:length(pbNc_1$X.Base) | 15 pbNc_1$id = 1:length(pbNc_1$X.Base) |
31 scale_x_continuous(breaks = pbNc_2$id, labels = pbNc_2$X.Base) + | 28 scale_x_continuous(breaks = pbNc_2$id, labels = pbNc_2$X.Base) + |
32 facet_grid(. ~ trim) + | 29 facet_grid(. ~ trim) + |
33 ylim(0, 1) + | 30 ylim(0, 1) + |
34 xlab('N-Count') + | 31 xlab('N-Count') + |
35 ylab('') + | 32 ylab('') + |
36 theme(axis.text.x = element_text(angle=45)) | 33 theme(axis.text.x = element_text(size = 5), |
34 axis.line = element_line(), | |
35 panel.background = element_rect(fill = NA)) | |
37 ggplotly(p) | 36 ggplotly(p) |
38 ``` | 37 ``` |