Mercurial > repos > mingchen0919 > aurora_fastqc_site

comparison 03_per_tile_sequence_quality.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 tile sequence quality 10 ### Per tile sequence quality
14 11
15 ```{r 'per tile sequence quality', fig.width=10} 12 ```{r 'per tile sequence quality', fig.width=10}
16 ## check if 'per tile sequence quality' module exits or not 13 ## check if 'per tile sequence quality' module exits or not
17 check_ptsq = grep('Per tile sequence quality', readLines(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'))) 14 check_ptsq = grep('Per tile sequence quality', readLines(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt')))
18 if (length(check_ptsq) > 0) { 15 if (length(check_ptsq) > 0) {
27 comb_ptsq = rbind(ptsq_1, ptsq_2) 24 comb_ptsq = rbind(ptsq_1, ptsq_2)
28 comb_ptsq$trim = factor(levels = c('before', 'after'), comb_ptsq$trim) 25 comb_ptsq$trim = factor(levels = c('before', 'after'), comb_ptsq$trim)
29 comb_ptsq$Base = factor(levels = unique(comb_ptsq$Base), comb_ptsq$Base) 26 comb_ptsq$Base = factor(levels = unique(comb_ptsq$Base), comb_ptsq$Base)
30 27
31 # convert integers to charaters 28 # convert integers to charaters
32 comb_ptsq$Tile = as.character(comb_ptsq$X.Tile) 29 # comb_ptsq$Tile = as.character(comb_ptsq$X.Tile)
33 30
34 p = ggplot(data = comb_ptsq, aes(x = Base, y = Tile, fill = Mean)) + 31 p = ggplot(data = comb_ptsq) +
35 geom_raster() + 32 geom_raster(mapping = aes(x = Base, y = X.Tile, fill = Mean)) +
36 facet_grid(. ~ trim) + 33 facet_grid(. ~ trim) +
37 xlab('Position in read (bp)') + 34 scale_x_discrete(name = "Position in read (bp)") +
38 ylab('') + 35 scale_y_continuous(name = "") +
39 theme(axis.text.x = element_text(angle=45)) 36 scale_fill_gradient(low = "blue", high = "red") +
37 theme(axis.text.x = element_text(size = 5, angle = 90),
38 axis.text.y = element_text(size = 5),
39 panel.background = element_rect(fill = NA))
40 ggplotly(p) 40 ggplotly(p)
41 } else { 41 } else {
42 print('No "per tile sequence quality" data') 42 print('No "per tile sequence quality" data')
43 } 43 }
44 ``` 44 ```