---
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 quality

```{r 'per base sequence quality', fig.width=10}
## reads 1
pbsq_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence quality')
pbsq_1$id = 1:length(pbsq_1$X.Base)
pbsq_1$trim = 'before'

## reads 2
pbsq_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence quality')
pbsq_2$id = 1:length(pbsq_2$X.Base)
pbsq_2$trim = 'after'

comb_pbsq = rbind(pbsq_1, pbsq_2)
comb_pbsq$trim = factor(levels = c('before', 'after'), comb_pbsq$trim)

p = ggplot(data = comb_pbsq) +
  geom_boxplot(mapping = aes(x = id, 
                             lower = Lower.Quartile, 
                             upper = Upper.Quartile, 
                             middle = Median, 
                             ymin = X10th.Percentile, 
                             ymax = X90th.Percentile,
                             fill = "yellow"),
               stat = 'identity') +
  geom_line(mapping = aes(x = id, y = Mean, color = "red")) +
  scale_x_continuous(name = 'Position in read (bp)', breaks = pbsq_2$id, labels = pbsq_2$X.Base) +
  scale_y_continuous(limits = c(0, max(comb_pbsq$Upper.Quartile) + 5)) +
  scale_fill_identity() +
  scale_color_identity() + 
  facet_grid(. ~ trim) +
  theme(axis.text.x = element_text(size = 5),
        panel.background = element_rect(fill = NA),
        panel.grid.major.y = element_line(color = 'blue', size = 0.1))
p
```