Mercurial > repos > mingchen0919 > aurora_fastqc_site
comparison 03_per_tile_sequence_quality.Rmd @ 0:b7c115edd970 draft
planemo upload
author | mingchen0919 |
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date | Tue, 27 Feb 2018 10:37:12 -0500 |
parents | |
children | c64267b9f754 |
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-1:000000000000 | 0:b7c115edd970 |
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1 --- | |
2 output: html_document | |
3 --- | |
4 | |
5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
6 knitr::opts_chunk$set( | |
7 echo = as.logical(opt$X_e), | |
8 error = TRUE, | |
9 eval = TRUE | |
10 ) | |
11 ``` | |
12 | |
13 # Per tile sequence quality | |
14 | |
15 ```{r 'per tile sequence quality', fig.width=10} | |
16 ## check if 'per tile sequence quality' module exits or not | |
17 check_ptsq = grep('Per tile sequence quality', readLines(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'))) | |
18 if (length(check_ptsq) > 0) { | |
19 ## reads 1 | |
20 ptsq_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per tile sequence quality') | |
21 ptsq_1$trim = 'before' | |
22 | |
23 ## reads 2 | |
24 ptsq_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per tile sequence quality') | |
25 ptsq_2$trim = 'after' | |
26 | |
27 comb_ptsq = rbind(ptsq_1, ptsq_2) | |
28 comb_ptsq$trim = factor(levels = c('before', 'after'), comb_ptsq$trim) | |
29 comb_ptsq$Base = factor(levels = unique(comb_ptsq$Base), comb_ptsq$Base) | |
30 | |
31 # convert integers to charaters | |
32 comb_ptsq$Tile = as.character(comb_ptsq$X.Tile) | |
33 | |
34 p = ggplot(data = comb_ptsq, aes(x = Base, y = Tile, fill = Mean)) + | |
35 geom_raster() + | |
36 facet_grid(. ~ trim) + | |
37 xlab('Position in read (bp)') + | |
38 ylab('') + | |
39 theme(axis.text.x = element_text(angle=45)) | |
40 ggplotly(p) | |
41 } else { | |
42 print('No "per tile sequence quality" data') | |
43 } | |
44 ``` |