Mercurial > repos > mingchen0919 > aurora_fastqc_site
comparison 04_per_sequence_quality_score.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 | |
14 # Per sequence quality score | |
15 | |
16 ```{r 'Per sequence quality score', fig.width=10} | |
17 ## reads 1 | |
18 psqs_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence quality scores') | |
19 psqs_1$trim = 'before' | |
20 | |
21 ## reads 2 | |
22 psqs_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per sequence quality scores') | |
23 psqs_2$trim = 'after' | |
24 | |
25 comb_psqs = rbind(psqs_1, psqs_2) | |
26 comb_psqs$trim = factor(levels = c('before', 'after'), comb_psqs$trim) | |
27 | |
28 p = ggplot(data = comb_psqs, aes(x = X.Quality, y = Count)) + | |
29 geom_line(color = 'red') + | |
30 facet_grid(. ~ trim) + | |
31 xlim(min(comb_psqs$X.Quality), max(comb_psqs$X.Quality)) + | |
32 xlab('Mean Sequence Qaulity (Phred Score)') + | |
33 ylab('') | |
34 ggplotly(p) | |
35 ``` |