diff 04_per_sequence_quality_score.Rmd @ 2:c64267b9f754 draft default tip

planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty

--- a/04_per_sequence_quality_score.Rmd	Tue Feb 27 10:40:20 2018 -0500
+++ b/04_per_sequence_quality_score.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 sequence quality score
+### Per sequence quality score
 
 ```{r 'Per sequence quality score', fig.width=10}
 ## reads 1
@@ -25,11 +21,15 @@
 comb_psqs = rbind(psqs_1, psqs_2)
 comb_psqs$trim = factor(levels = c('before', 'after'), comb_psqs$trim)
 
-p = ggplot(data = comb_psqs, aes(x = X.Quality, y = Count)) + 
-  geom_line(color = 'red') + 
+p = ggplot(data = comb_psqs) + 
+  geom_line(mapping = aes(x = X.Quality, y = Count), color = 'red') + 
   facet_grid(. ~ trim) + 
-  xlim(min(comb_psqs$X.Quality), max(comb_psqs$X.Quality)) + 
-  xlab('Mean Sequence Qaulity (Phred Score)') + 
-  ylab('')
-ggplotly(p)
+  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
 ```
+