diff 06_per_sequence_gc_content.Rmd @ 11:507eec497730 draft

update fastqc site

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/06_per_sequence_gc_content.Rmd	Tue Nov 07 16:52:24 2017 -0500
@@ -0,0 +1,38 @@
+---
+title: 'Per sequence GC content'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO,
+  error = TRUE
+)
+```
+
+### Per sequence GC content
+
+```{r 'Per sequence GC content', fig.width=10}
+## reads 1
+psGCc_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per sequence GC content')
+psGCc_1$trim = 'before'
+
+## reads 2
+psGCc_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per sequence GC content')
+psGCc_2$trim = 'after'
+
+comb_psGCc = rbind(psGCc_1, psGCc_2)
+comb_psGCc$trim = factor(levels = c('before', 'after'), comb_psGCc$trim)
+
+p = ggplot(data = comb_psGCc, aes(x = X.GC.Content, y = Count)) +
+  geom_line(color = 'red') +
+  facet_grid(. ~ trim) +
+  xlab('Mean Sequence Qaulity (Phred Score)') +
+  ylab('')
+ggplotly(p)
+```
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