--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/09_sequence_duplication_levels.Rmd	Tue Feb 27 10:37:12 2018 -0500
@@ -0,0 +1,45 @@
+---
+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$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#')
+names(sdl_1) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total')
+sdl_1$id = 1:length(sdl_1$Duplication_Level)
+
+melt_sdl_1 = melt(sdl_1, id=c('Duplication_Level', 'id'))
+melt_sdl_1$trim = 'before'
+
+
+## reads 2
+sdl_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Duplication Levels', header = FALSE, comment.char = '#')
+names(sdl_2) = c('Duplication_Level', 'Percentage_of_deduplicated', 'Percentage_of_total')
+sdl_2$id = 1:length(sdl_2$Duplication_Level)
+
+melt_sdl_2 = melt(sdl_2, id=c('Duplication_Level', 'id'))
+melt_sdl_2$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)
+```
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