--- a/05_per_base_sequence_content.Rmd	Tue Feb 27 10:40:20 2018 -0500
+++ b/05_per_base_sequence_content.Rmd	Sun Dec 30 12:48:14 2018 -0500
@@ -3,15 +3,11 @@
 ---
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = as.logical(opt$X_e),
-  error = TRUE,
-  eval = TRUE
-)
+knitr::opts_knit$set(progress = FALSE)
+knitr::opts_chunk$set(error = TRUE, echo = FALSE)
 ```
 
-
-# Per base sequence content
+### Per base sequence content
 
 ```{r 'Per base sequence content', fig.width=10}
 ## reads 1
@@ -32,12 +28,14 @@
 comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2)
 comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim)
 
-p = ggplot(data = comb_pbsc, aes(x = id, y = value, color = variable)) +
-  geom_line() +
+p = ggplot(data = comb_pbsc) +
+  geom_line(mapping = aes(x = id, y = value, color = variable)) +
   facet_grid(. ~ trim) +
   xlim(min(comb_pbsc$id), max(comb_pbsc$id)) + 
   ylim(0, 100) +
   xlab('Position in read (bp)') +
-  ylab('')
+  ylab('') +
+  scale_color_discrete(name = '') +
+  theme_classic()
 ggplotly(p)
-```
\ No newline at end of file
+```