view 05_per_base_sequence_content.Rmd @ 2:c64267b9f754 draft default tip

planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty

---
output: html_document
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_knit$set(progress = FALSE)
knitr::opts_chunk$set(error = TRUE, echo = FALSE)
```

### Per base sequence content

```{r 'Per base sequence content', fig.width=10}
## reads 1
pbsc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence content')
pbsc_1$id = 1:length(pbsc_1$X.Base)

melt_pbsc_1 = melt(pbsc_1, id=c('X.Base', 'id'))
melt_pbsc_1$trim = 'before'


## reads 2
pbsc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence content')
pbsc_2$id = 1:length(pbsc_2$X.Base)

melt_pbsc_2 = melt(pbsc_2, id=c('X.Base', 'id'))
melt_pbsc_2$trim = 'after'

comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2)
comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim)

p = ggplot(data = comb_pbsc) +
  geom_line(mapping = aes(x = id, y = value, color = variable)) +
  facet_grid(. ~ trim) +
  xlim(min(comb_pbsc$id), max(comb_pbsc$id)) + 
  ylim(0, 100) +
  xlab('Position in read (bp)') +
  ylab('') +
  scale_color_discrete(name = '') +
  theme_classic()
ggplotly(p)
```