diff 08_sequence_length_distribution.Rmd @ 1:645291efd2e7 draft

working version

--- a/08_sequence_length_distribution.Rmd	Tue Feb 27 00:39:56 2018 -0500
+++ b/08_sequence_length_distribution.Rmd	Tue Feb 27 10:36:24 2018 -0500
@@ -0,0 +1,37 @@
+---
+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 Length Distribution
+
+```{r 'Sequence Length Distribution', fig.width=10}
+## reads 1
+sld_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Sequence Length Distribution')
+sld_1$id = 1:length(sld_1$X.Length)
+sld_1$trim = 'before'
+
+## reads 2
+sld_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Sequence Length Distribution')
+sld_2$id = 1:length(sld_2$X.Length)
+sld_2$trim = 'after'
+
+comb_sld = rbind(sld_1, sld_2)
+comb_sld$trim = factor(levels = c('before', 'after'), comb_sld$trim)
+
+p = ggplot(data = comb_sld, aes(x = id, y = Count)) +
+  geom_line(color = 'red') +
+  scale_x_continuous(breaks = sld_2$id, labels = sld_2$X.Length) + 
+  facet_grid(. ~ trim) +
+  xlab('Sequence Length (bp)') +
+  ylab('') + 
+  theme(axis.text.x = element_text(angle=45))
+ggplotly(p)
+```
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