diff 04_per_sequence_quality_score.Rmd @ 0:b7c115edd970 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/04_per_sequence_quality_score.Rmd	Tue Feb 27 10:37:12 2018 -0500
@@ -0,0 +1,35 @@
+---
+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 sequence quality score
+
+```{r 'Per sequence quality score', fig.width=10}
+## reads 1
+psqs_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per sequence quality scores')
+psqs_1$trim = 'before'
+
+## reads 2
+psqs_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per sequence quality scores')
+psqs_2$trim = 'after'
+
+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') + 
+  facet_grid(. ~ trim) + 
+  xlim(min(comb_psqs$X.Quality), max(comb_psqs$X.Quality)) + 
+  xlab('Mean Sequence Qaulity (Phred Score)') + 
+  ylab('')
+ggplotly(p)
+```