--- a/09_sequence_duplication_levels.Rmd	Tue Feb 27 10:40:20 2018 -0500
+++ b/09_sequence_duplication_levels.Rmd	Sun Dec 30 12:48:14 2018 -0500
@@ -3,15 +3,12 @@
 ---
 
 ```{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)
 ```
 
 
-# Sequence Duplication Levels
+### Sequence Duplication Levels
 
 ```{r 'Sequence Duplication Levels', fig.width=10}
 ## reads 1
@@ -34,12 +31,15 @@
 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() +
+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('') + 
-  theme(axis.text.x = element_text(angle=45))
-ggplotly(p)
-```
\ No newline at end of file
+  scale_color_discrete(name = '') +
+  theme(axis.text.x = element_text(size = 5),
+        panel.background = element_rect(fill = NA),
+        axis.line = element_line())
+p
+```