diff 03_per_tile_sequence_quality.Rmd @ 11:507eec497730 draft

update fastqc site

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/03_per_tile_sequence_quality.Rmd	Tue Nov 07 16:52:24 2017 -0500
@@ -0,0 +1,48 @@
+---
+title: 'Per Tile Sequence Quality'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO,
+  error = TRUE
+)
+```
+
+### Per tile sequence quality
+
+```{r 'per tile sequence quality', fig.width=10}
+## check if 'per tile sequence quality' module exits or not
+check_ptsq = grep('Per tile sequence quality', readLines('REPORT_DIR/reads_1_fastqc_data.txt'))
+if (length(check_ptsq) > 0) {
+    ## reads 1
+  ptsq_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per tile sequence quality')
+  ptsq_1$trim = 'before'
+  
+  ## reads 2
+  ptsq_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per tile sequence quality')
+  ptsq_2$trim = 'after'
+  
+  comb_ptsq = rbind(ptsq_1, ptsq_2)
+  comb_ptsq$trim = factor(levels = c('before', 'after'), comb_ptsq$trim)
+  comb_ptsq$Base = factor(levels = unique(comb_ptsq$Base), comb_ptsq$Base)
+  
+  # convert integers to charaters
+  comb_ptsq$Tile = as.character(comb_ptsq$X.Tile)
+  
+  p = ggplot(data = comb_ptsq, aes(x = Base, y = Tile, fill = Mean)) +
+    geom_raster() + 
+    facet_grid(. ~ trim) + 
+    xlab('Position in read (bp)') + 
+    ylab('') +
+    theme(axis.text.x = element_text(angle=45))
+  ggplotly(p)
+} else {
+  print('No "per tile sequence quality" data')
+}
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