Mercurial > repos > mingchen0919 > aurora_fastqc_site

comparison 08_sequence_length_distribution.Rmd @ 0:b7c115edd970 draft

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planemo upload
author mingchen0919
date Tue, 27 Feb 2018 10:37:12 -0500
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children c64267b9f754
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-1:000000000000 0:b7c115edd970
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 # Sequence Length Distribution
14
15 ```{r 'Sequence Length Distribution', fig.width=10}
16 ## reads 1
17 sld_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Length Distribution')
18 sld_1$id = 1:length(sld_1$X.Length)
19 sld_1$trim = 'before'
20
21 ## reads 2
22 sld_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Length Distribution')
23 sld_2$id = 1:length(sld_2$X.Length)
24 sld_2$trim = 'after'
25
26 comb_sld = rbind(sld_1, sld_2)
27 comb_sld$trim = factor(levels = c('before', 'after'), comb_sld$trim)
28
29 p = ggplot(data = comb_sld, aes(x = id, y = Count)) +
30 geom_line(color = 'red') +
31 scale_x_continuous(breaks = sld_2$id, labels = sld_2$X.Length) +
32 facet_grid(. ~ trim) +
33 xlab('Sequence Length (bp)') +
34 ylab('') +
35 theme(axis.text.x = element_text(angle=45))
36 ggplotly(p)
37 ```