diff 4_per_sequence_GC_content.Rmd @ 0:d732d4526c6d draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/4_per_sequence_GC_content.Rmd	Tue Aug 08 10:14:46 2017 -0400
@@ -0,0 +1,38 @@
+---
+title: "Per Sequence GC Content"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+## Per Sequence GC Content
+
+
+```{r}
+PSGC_df = data.frame()
+PSGC_file_paths = read.csv('PSGC_file_paths.txt', 
+                           header = TRUE, stringsAsFactors = FALSE)
+for(i in 1:nrow(PSGC_file_paths)) {
+  # file_path = paste0('REPORT_OUTPUT_DIR/', PSGC_file_paths[i,2])
+  file_path = PSGC_file_paths[i,2]
+  psgc_df = read.csv(file_path,
+                     sep='\t', header=TRUE, stringsAsFactors = FALSE) 
+  psgc_df$sample_id = rep(PSGC_file_paths[i,1], nrow(psgc_df))
+  PSGC_df = rbind(PSGC_df, psgc_df)
+}
+```
+
+
+```{r}
+max_phred = max(PSGC_df$Count) + 5
+hchart(PSGC_df, "line", hcaes(x = X.GC.Content, y = Count, group = sample_id)) %>%
+  hc_title(
+    text = "Per Sequence GC Content"
+  ) %>%
+  hc_xAxis(
+    title = list(text = "% GC")
+  ) %>%
+  hc_exporting(enabled = TRUE)
+```