In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

knitr::opts_chunk$set(echo = FALSE)
library(ezRun)
library(ggplot2)
library(tidyr)
## debug
#title: "`r paste(:'PBSV', params$sample`)"
#wddir <- "/misc/GT/analysis/qiwei/debug/p26994/pbsv_2023-05-10--09-34-19"
wddir <- "."
#params = list(sample="NA24385")
## end of debug

Result {.tabset}

Overview

params$sample

dat.file <- file.path(wddir, paste0(params$sample,".SURVIVOR.log"))
dat <- readLines(dat.file)
counts <- data.frame( Count=c(scan(text=dat[4], what="")[1], scan(text=dat[4], what="")[2], scan(text=dat[4], what="")[3], scan(text=dat[4], what="")[4], scan(text=dat[4], what="")[5], scan(text=dat[4], what="")[6]))
row.names(counts)<-c("Tot", "DEL", "DUP", "INS", "INV", "TRA")
library(knitr)
kable(counts, caption = "Summary stats")
barplot(t(as.matrix(counts)), main="Summary stats", cex.main=0.7, cex.names=0.7, las=2)

SV types by length

  tbl<-read.table(paste0(wddir, "/", params$sample, ".stats.txt"), header=TRUE)
  data_long<- gather(tbl, svType, Count, Del:TRA, factor_key=TRUE)
  data_long$Len<-factor(data_long$Len, levels = c("0-50bp", "50-100bp", "100-1000bp", "1000-10000bp", "10000+bp"))
  p1<-ggplot(data=data_long, aes(x=Len, y=Count, color=svType, fill=svType))
  p1<-p1 + geom_bar(stat="identity")
  p1<-p1 + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
  p1<-p1 + facet_grid(. ~ svType) + scale_y_continuous(trans='log10') + ggtitle(params$sample)
  #pdf(paste0(outPath, "/", sampleName, '.stats.pdf'))
        print(p1)
  #dev.off()

SV types by chr

  df<-read.table(paste0(wddir, "/", params$sample, ".stats.txt_CHR"), header=TRUE)
  df_long<- gather(df, svType, Count, DEL:TRA, factor_key=TRUE)
  df_long$Chr<-factor(df_long$Chr, levels = c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "Y", "MT", "GL000195.1", "GL000205.1", "GL000214.1", "GL000220.1", "GL000224.1", "GL000226.1"))
  p1<-ggplot(data=df_long, aes(x=Chr, y=Count, color=svType, fill=svType))
  p1<-p1 + geom_bar(stat="identity")
  p1<-p1 + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
  p1<-p1 + ggtitle(params$sample)
  #pdf(paste0(outPath, "/", sampleName, '.stats.pdf'))
        print(p1)
  #dev.off()