diff 10_adapter_content.Rmd @ 11:507eec497730 draft

update fastqc site

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/10_adapter_content.Rmd	Tue Nov 07 16:52:24 2017 -0500
@@ -0,0 +1,46 @@
+---
+title: 'Adapter Content'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO,
+  error = TRUE
+)
+```
+
+### Adapter Content
+
+```{r 'Adapter Content', fig.width=10}
+## reads 1
+ac_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Adapter Content')
+ac_1$id = 1:length(ac_1$X.Position)
+
+melt_ac_1 = melt(ac_1, id=c('X.Position', 'id'))
+melt_ac_1$trim = 'before'
+
+## reads 2
+ac_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Adapter Content')
+ac_2$id = 1:length(ac_2$X.Position)
+
+melt_ac_2 = melt(ac_2, id=c('X.Position', 'id'))
+melt_ac_2$trim = 'after'
+
+comb_ac = rbind(melt_ac_1, melt_ac_2)
+comb_ac$trim = factor(levels = c('before', 'after'), comb_ac$trim)
+
+p = ggplot(data = comb_ac, aes(x = id, y = value, color = variable)) +
+  geom_line() +
+  facet_grid(. ~ trim) +
+  xlim(min(comb_ac$id), max(comb_ac$id)) + 
+  ylim(0, 1) +
+  xlab('Position in read (bp)') +
+  ylab('')
+ggplotly(p)
+```
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