Mercurial > repos > mingchen0919 > aurora_fastqc_site

comparison 06_per_sequence_gc_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
equal deleted inserted replaced
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 sequence GC content 10 ### Per sequence GC content
14 11
15 ```{r 'Per sequence GC content', fig.width=10} 12 ```{r 'Per sequence GC content', fig.width=10}
16 ## reads 1 13 ## reads 1
17 psGCc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence GC content') 14 psGCc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence GC content')
18 psGCc_1$trim = 'before' 15 psGCc_1$trim = 'before'
26 23
27 p = ggplot(data = comb_psGCc, aes(x = X.GC.Content, y = Count)) + 24 p = ggplot(data = comb_psGCc, aes(x = X.GC.Content, y = Count)) +
28 geom_line(color = 'red') + 25 geom_line(color = 'red') +
29 facet_grid(. ~ trim) + 26 facet_grid(. ~ trim) +
30 xlab('Mean Sequence Qaulity (Phred Score)') + 27 xlab('Mean Sequence Qaulity (Phred Score)') +
31 ylab('') 28 ylab('') +
29 scale_color_discrete(name = '') +
30 theme_classic()
32 ggplotly(p) 31 ggplotly(p)
33 ``` 32 ```