Mercurial > repos > mingchen0919 > aurora_fastqc_site

comparison 10_adapter_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 # Adapter Content 10 ### Adapter Content
14 11
15 ```{r 'Adapter Content', fig.width=10} 12 ```{r 'Adapter Content', fig.width=10}
16 ## reads 1 13 ## reads 1
17 ac_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Adapter Content') 14 ac_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Adapter Content')
18 ac_1$id = 1:length(ac_1$X.Position) 15 ac_1$id = 1:length(ac_1$X.Position)
34 geom_line() + 31 geom_line() +
35 facet_grid(. ~ trim) + 32 facet_grid(. ~ trim) +
36 xlim(min(comb_ac$id), max(comb_ac$id)) + 33 xlim(min(comb_ac$id), max(comb_ac$id)) +
37 ylim(0, 1) + 34 ylim(0, 1) +
38 xlab('Position in read (bp)') + 35 xlab('Position in read (bp)') +
39 ylab('') 36 ylab('') +
37 scale_color_discrete(name = '') +
38 theme(axis.text.x = element_text(size = 5),
39 panel.background = element_rect(fill = NA),
40 axis.line = element_line())
40 ggplotly(p) 41 ggplotly(p)
41 ``` 42 ```