Mercurial > repos > mingchen0919 > aurora_fastqc_site

comparison 07_per_base_n_content.Rmd @ 2:c64267b9f754 draft default tip

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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 12:48:14 -0500
parents b7c115edd970
children
comparison
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1:92e3de11b9f8 2:c64267b9f754
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 ```