Mercurial > repos > mingchen0919 > aurora_fastqc_site
annotate 08_sequence_length_distribution.Rmd @ 10:5286f3b1c9c2 draft default tip
planemo upload commit 363ef0a73d874c67326a67f51a78328906951248-dirty
| author | mingchen0919 |
|---|---|
| date | Fri, 30 Nov 2018 22:15:50 -0500 |
| parents | 94762f1cb779 |
| children |
| rev | line source |
|---|---|
| 1 | 1 --- |
| 2 output: html_document | |
| 3 --- | |
| 4 | |
| 5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
|
8
94762f1cb779
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
mingchen0919
parents:
3
diff
changeset
|
6 knitr::opts_knit$set(progress = FALSE) |
|
94762f1cb779
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
mingchen0919
parents:
3
diff
changeset
|
7 knitr::opts_chunk$set(error = TRUE, echo = FALSE) |
| 1 | 8 ``` |
| 9 | |
| 3 | 10 ### Sequence Length Distribution |
| 1 | 11 |
| 12 ```{r 'Sequence Length Distribution', fig.width=10} | |
| 13 ## reads 1 | |
| 14 sld_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Length Distribution') | |
| 15 sld_1$id = 1:length(sld_1$X.Length) | |
| 16 sld_1$trim = 'before' | |
| 17 | |
| 18 ## reads 2 | |
| 19 sld_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Length Distribution') | |
| 20 sld_2$id = 1:length(sld_2$X.Length) | |
| 21 sld_2$trim = 'after' | |
| 22 | |
| 23 comb_sld = rbind(sld_1, sld_2) | |
| 24 comb_sld$trim = factor(levels = c('before', 'after'), comb_sld$trim) | |
| 25 | |
| 26 p = ggplot(data = comb_sld, aes(x = id, y = Count)) + | |
| 27 geom_line(color = 'red') + | |
| 28 scale_x_continuous(breaks = sld_2$id, labels = sld_2$X.Length) + | |
| 29 facet_grid(. ~ trim) + | |
| 30 xlab('Sequence Length (bp)') + | |
| 31 ylab('') + | |
| 3 | 32 theme(axis.text.x = element_text(size = 5), |
| 33 panel.background = element_rect(fill = NA), | |
| 34 axis.line = element_line(), | |
| 35 plot.margin = margin(2,2,2,10) ) | |
| 1 | 36 ggplotly(p) |
| 37 ``` |