Mercurial > repos > mingchen0919 > aurora_fastqc_site
comparison 04_per_sequence_quality_score.Rmd @ 2:c64267b9f754 draft default tip
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author | mingchen0919 |
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date | Sun, 30 Dec 2018 12:48:14 -0500 |
parents | b7c115edd970 |
children |
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1:92e3de11b9f8 | 2:c64267b9f754 |
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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 ### Per sequence quality score |
14 # Per sequence quality score | |
15 | 11 |
16 ```{r 'Per sequence quality score', fig.width=10} | 12 ```{r 'Per sequence quality score', fig.width=10} |
17 ## reads 1 | 13 ## reads 1 |
18 psqs_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence quality scores') | 14 psqs_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence quality scores') |
19 psqs_1$trim = 'before' | 15 psqs_1$trim = 'before' |
23 psqs_2$trim = 'after' | 19 psqs_2$trim = 'after' |
24 | 20 |
25 comb_psqs = rbind(psqs_1, psqs_2) | 21 comb_psqs = rbind(psqs_1, psqs_2) |
26 comb_psqs$trim = factor(levels = c('before', 'after'), comb_psqs$trim) | 22 comb_psqs$trim = factor(levels = c('before', 'after'), comb_psqs$trim) |
27 | 23 |
28 p = ggplot(data = comb_psqs, aes(x = X.Quality, y = Count)) + | 24 p = ggplot(data = comb_psqs) + |
29 geom_line(color = 'red') + | 25 geom_line(mapping = aes(x = X.Quality, y = Count), color = 'red') + |
30 facet_grid(. ~ trim) + | 26 facet_grid(. ~ trim) + |
31 xlim(min(comb_psqs$X.Quality), max(comb_psqs$X.Quality)) + | 27 scale_x_continuous(name = 'Mean Sequence Qaulity (Phred Score)', |
32 xlab('Mean Sequence Qaulity (Phred Score)') + | 28 limits = c(min(comb_psqs$X.Quality), max(comb_psqs$X.Quality))) + |
33 ylab('') | 29 scale_y_continuous(name = '') + |
34 ggplotly(p) | 30 theme(panel.background = element_rect(fill = NA), |
31 axis.line = element_line(), | |
32 panel.grid.major.y = element_line(color = 'blue', size = 0.1)) | |
33 p | |
35 ``` | 34 ``` |
35 |