Mercurial > repos > mingchen0919 > aurora_fastqc_site

comparison 09_sequence_duplication_levels.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 10
14 # Sequence Duplication Levels 11 ### Sequence Duplication Levels
15 12
16 ```{r 'Sequence Duplication Levels', fig.width=10} 13 ```{r 'Sequence Duplication Levels', fig.width=10}
17 ## reads 1 14 ## reads 1
18 sdl_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#') 15 sdl_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#')
19 names(sdl_1) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total') 16 names(sdl_1) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total')
32 melt_sdl_2$trim = 'after' 29 melt_sdl_2$trim = 'after'
33 30
34 comb_sdl = rbind(melt_sdl_1, melt_sdl_2) 31 comb_sdl = rbind(melt_sdl_1, melt_sdl_2)
35 comb_sdl$trim = factor(levels = c('before', 'after'), comb_sdl$trim) 32 comb_sdl$trim = factor(levels = c('before', 'after'), comb_sdl$trim)
36 33
37 p = ggplot(data = comb_sdl, aes(x = id, y = value, color = variable)) + 34 p = ggplot(data = comb_sdl) +
38 geom_line() + 35 geom_line(mapping = aes(x = id, y = value, color = variable)) +
39 scale_x_continuous(breaks = sdl_2$id, labels = sdl_2$Duplication_Level) + 36 scale_x_continuous(breaks = sdl_2$id, labels = sdl_2$Duplication_Level) +
40 facet_grid(. ~ trim) + 37 facet_grid(. ~ trim) +
41 xlab('Sequence Duplication Level') + 38 xlab('Sequence Duplication Level') +
42 ylab('') + 39 ylab('') +
43 theme(axis.text.x = element_text(angle=45)) 40 scale_color_discrete(name = '') +
44 ggplotly(p) 41 theme(axis.text.x = element_text(size = 5),
42 panel.background = element_rect(fill = NA),
43 axis.line = element_line())
44 p
45 ``` 45 ```