comparison 10_adapter_content.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
)
```

# Adapter Content

```{r 'Adapter Content', fig.width=10}
## reads 1
ac_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Adapter Content')
ac_1$id = 1:length(ac_1$X.Position)

  geom_line() +
  facet_grid(. ~ trim) +
  xlim(min(comb_ac$id), max(comb_ac$id)) + 
  ylim(0, 1) +
  xlab('Position in read (bp)') +
  ylab('')
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)
```

### Adapter Content

```{r 'Adapter Content', fig.width=10}
## reads 1
ac_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Adapter Content')
ac_1$id = 1:length(ac_1$X.Position)

  geom_line() +
  facet_grid(. ~ trim) +
  xlim(min(comb_ac$id), max(comb_ac$id)) + 
  ylim(0, 1) +
  xlab('Position in read (bp)') +
  ylab('') +
  scale_color_discrete(name = '') +
  theme(axis.text.x = element_text(size = 5),
        panel.background = element_rect(fill = NA),
        axis.line = element_line())
ggplotly(p)
```