diff 07_per_base_n_content.Rmd @ 0:b7c115edd970 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/07_per_base_n_content.Rmd	Tue Feb 27 10:37:12 2018 -0500
@@ -0,0 +1,38 @@
+---
+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
+)
+```
+
+# Per base N content
+
+```{r 'Per base N content', fig.width=10}
+## reads 1
+pbNc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base N content')
+pbNc_1$id = 1:length(pbNc_1$X.Base)
+pbNc_1$trim = 'before'
+
+## reads 2
+pbNc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base N content')
+pbNc_2$id = 1:length(pbNc_2$X.Base)
+pbNc_2$trim = 'after'
+
+comb_pbNc = rbind(pbNc_1, pbNc_2)
+comb_pbNc$trim = factor(levels = c('before', 'after'), comb_pbNc$trim)
+
+p = ggplot(data = comb_pbNc, aes(x = id, y = N.Count)) +
+  geom_line(color = 'red') +
+  scale_x_continuous(breaks = pbNc_2$id, labels = pbNc_2$X.Base) + 
+  facet_grid(. ~ trim) +
+  ylim(0, 1) + 
+  xlab('N-Count') +
+  ylab('') + 
+  theme(axis.text.x = element_text(angle=45))
+ggplotly(p)
+```
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