diff 2_per_base_N_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/2_per_base_N_content.Rmd	Tue Aug 08 10:14:46 2017 -0400
@@ -0,0 +1,58 @@
+---
+title: "Per Base N Content"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+## Per Base N Content
+
+```{r}
+PBNC_df = data.frame()
+PBNC_file_paths = read.csv('PBNC_file_paths.txt',
+                           header = TRUE, stringsAsFactors = FALSE)
+for(i in 1:nrow(PBNC_file_paths)) {
+  # file_path = paste0('REPORT_OUTPUT_DIR/', PBNC_file_paths[i,2])
+  file_path = PBNC_file_paths[i,2]
+  pbnc_df = read.csv(file_path,
+                     sep='\t', header=TRUE, stringsAsFactors = FALSE) %>%
+    mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]),
+           Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>%
+  (function (df) {
+    df1 = select(df, -Base2)
+    df2 = select(df, -Base1) %>% filter(Base2 != '')
+    colnames(df1) = c(colnames(df1)[1:2], 'Base')
+    colnames(df2) = c(colnames(df2)[1:2], 'Base')
+    res = rbind(df1, df2) %>% arrange(Base)
+    return(res)
+  })
+  pbnc_df$sample_id = rep(PBNC_file_paths[i,1], nrow(pbnc_df))
+  PBNC_df = rbind(PBNC_df, pbnc_df)
+}
+```
+
+
+```{r}
+PBNC_df$N.Count = PBNC_df$N.Count * 100
+max_phred = max(PBNC_df$N.Count) + 5
+hchart(PBNC_df, "line", hcaes(x = as.character(Base), y = N.Count, group = sample_id)) %>%
+  hc_title(
+    text = "Per Base N Content"
+  ) %>%
+  hc_xAxis(
+    title = list(text = "Base Position")
+  ) %>%
+  hc_yAxis(
+    title = list(text = "N %"),
+    plotLines = list(
+      list(label = list(text = "N = 5%"),
+           width = 2,
+           dashStyle = "dash",
+           color = "red",
+           value = 5)
+    )
+  ) %>% 
+  hc_exporting(enabled = TRUE)
+```