view 02_per_base_sequence_quality.Rmd @ 11:507eec497730 draft

update fastqc site

---
title: 'Per base sequence quality'
output:
    html_document:
      number_sections: true
      toc: true
      theme: cosmo
      highlight: tango
---

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

### Per base sequence quality

```{r 'per base sequence quality', fig.width=10}
## reads 1
pbsq_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per base sequence quality')
pbsq_1$id = 1:length(pbsq_1$X.Base)

melt_pbsq_1 = filter(melt(pbsq_1, id=c('X.Base', 'id')), variable == 'Mean')
melt_pbsq_1$trim = 'before'


## reads 2
pbsq_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per base sequence quality')
pbsq_2$id = 1:length(pbsq_2$X.Base)

melt_pbsq_2 = filter(melt(pbsq_2, id=c('X.Base', 'id')), variable == 'Mean')
melt_pbsq_2$trim = 'after'

comb_pbsq = rbind(melt_pbsq_1, melt_pbsq_2)
comb_pbsq$trim = factor(levels = c('before', 'after'), comb_pbsq$trim)

p = ggplot(data = comb_pbsq) +
  geom_line(mapping = aes(x = id, y = value, group = variable, color = variable)) +
  scale_x_continuous(breaks = pbsq_2$id, labels = pbsq_2$X.Base) + 
  facet_grid(. ~ trim) + 
  ylim(0, max(comb_pbsq$value) + 5) +
  theme(axis.text.x = element_text(angle=45))
ggplotly(p)

```