---
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)
```

### Sequence Length Distribution

```{r 'Sequence Length Distribution', fig.width=10}
## reads 1
sld_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Length Distribution')
sld_1$id = 1:length(sld_1$X.Length)
sld_1$trim = 'before'

## reads 2
sld_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Length Distribution')
sld_2$id = 1:length(sld_2$X.Length)
sld_2$trim = 'after'

comb_sld = rbind(sld_1, sld_2)
comb_sld$trim = factor(levels = c('before', 'after'), comb_sld$trim)

p = ggplot(data = comb_sld, aes(x = id, y = Count)) +
  geom_line(color = 'red') +
  scale_x_continuous(breaks = sld_2$id, labels = sld_2$X.Length) + 
  facet_grid(. ~ trim) +
  xlab('Sequence Length (bp)') +
  ylab('') + 
  theme(axis.text.x = element_text(size = 5),
        panel.background = element_rect(fill = NA),
        axis.line = element_line(), 
        plot.margin = margin(2,2,2,10) )
ggplotly(p)
```