view 06_per_sequence_gc_content.Rmd @ 3:b9c9d1dacda6 draft

reformat code

---
output: html_document
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = as.logical(opt$X_e),
  error = TRUE,
  eval = TRUE
)
```

### Per sequence GC content

```{r 'Per sequence GC content', fig.width=10}
## reads 1
psGCc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence GC content')
psGCc_1$trim = 'before'

## reads 2
psGCc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per sequence GC content')
psGCc_2$trim = 'after'

comb_psGCc = rbind(psGCc_1, psGCc_2)
comb_psGCc$trim = factor(levels = c('before', 'after'), comb_psGCc$trim)

p = ggplot(data = comb_psGCc, aes(x = X.GC.Content, y = Count)) +
  geom_line(color = 'red') +
  facet_grid(. ~ trim) +
  xlab('Mean Sequence Qaulity (Phred Score)') +
  ylab('') +
  scale_color_discrete(name = '') +
  theme_classic()
ggplotly(p)
```