comparison 09_sequence_duplication_levels.Rmd @ 2:c64267b9f754 draft default tip

planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty

1:92e3de11b9f8

---
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
)
```


# Sequence Duplication Levels

```{r 'Sequence Duplication Levels', fig.width=10}
## reads 1
sdl_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#')
names(sdl_1) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total')

melt_sdl_2$trim = 'after'

comb_sdl = rbind(melt_sdl_1, melt_sdl_2)
comb_sdl$trim = factor(levels = c('before', 'after'), comb_sdl$trim)

p = ggplot(data = comb_sdl, aes(x = id, y = value, color = variable)) +
  geom_line() +
  scale_x_continuous(breaks = sdl_2$id, labels = sdl_2$Duplication_Level) +
  facet_grid(. ~ trim) +
  xlab('Sequence Duplication Level') +
  ylab('') + 
  theme(axis.text.x = element_text(angle=45))
ggplotly(p)
```

2:c64267b9f754

---
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 Duplication Levels

```{r 'Sequence Duplication Levels', fig.width=10}
## reads 1
sdl_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#')
names(sdl_1) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total')

melt_sdl_2$trim = 'after'

comb_sdl = rbind(melt_sdl_1, melt_sdl_2)
comb_sdl$trim = factor(levels = c('before', 'after'), comb_sdl$trim)

p = ggplot(data = comb_sdl) +
  geom_line(mapping = aes(x = id, y = value, color = variable)) +
  scale_x_continuous(breaks = sdl_2$id, labels = sdl_2$Duplication_Level) +
  facet_grid(. ~ trim) +
  xlab('Sequence Duplication Level') +
  ylab('') + 
  scale_color_discrete(name = '') +
  theme(axis.text.x = element_text(size = 5),
        panel.background = element_rect(fill = NA),
        axis.line = element_line())
p
```