annotate 04_per_sequence_quality_score.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 sequence quality score

```{r 'Per sequence quality score', fig.width=10}
## reads 1
psqs_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence quality scores')
psqs_1$trim = 'before'

## reads 2
psqs_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per sequence quality scores')
psqs_2$trim = 'after'

comb_psqs = rbind(psqs_1, psqs_2)
comb_psqs$trim = factor(levels = c('before', 'after'), comb_psqs$trim)

p = ggplot(data = comb_psqs) + 
  geom_line(mapping = aes(x = X.Quality, y = Count), color = 'red') + 
  facet_grid(. ~ trim) + 
  scale_x_continuous(name = 'Mean Sequence Qaulity (Phred Score)',
                     limits = c(min(comb_psqs$X.Quality), max(comb_psqs$X.Quality))) +
  scale_y_continuous(name = '') +
  theme(panel.background = element_rect(fill = NA),
        axis.line = element_line(),
        panel.grid.major.y = element_line(color = 'blue', size = 0.1))
p
```