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

knitr::opts_chunk$set(echo = TRUE)
require(ezRun)
require(knitr)
require(kableExtra)
require(plotly)
library(SummarizedExperiment)
library(webshot)
library(htmlwidgets)
library(tidyverse)
library(readxl)

output <- readRDS("output.rds")
param <- readRDS("param.rds")
input <- readRDS("input.rds")
gt <- readRDS("gt.rds")
chromSizes <- readRDS("chromSizes.rds")
dataset = input$meta
samples = input$getNames()

conds = ezConditionsFromDataset(dataset, param=param)
sampleColors = getSampleColors(conds, colorNames = names(conds))

Started on r format(Sys.time(), "%Y-%m-%d %H:%M:%S")

Mpileup {.tabset}

Sample Clustering

idxMat = ezMatrix(match(gt, c("0/0", "0/1", "1/1")) -2, rows=rownames(gt), cols=colnames(gt))
d = dist(t(idxMat))
if (all(!is.na(d))){
  hc=hclust(d, method="ward.D2" );
  hcd = as.dendrogram(hclust(d, method="ward.D2"), hang=-0.1)
  hcd = colorClusterLabels(hcd, sampleColors)
  par(cex=1.3, mar=c(12, 4.1, 4.1, 2.1))
  plot(hcd, main="Cluster by Genotype", xlab="")
}

Variants by Chromosomes

chrom = sub(":.*", "", rownames(gt))
pos = as.integer(sub("_.*", "", sub(".*:", "", rownames(gt))))
isRealChrom = !grepl("[\\._]", names(chromSizes)) & chromSizes > 20000 ## TODO select chromosomes by name
idxList = split(1:nrow(gt), chrom)
snpColors = c("0/0"="blue", "0/1"="darkgrey", "1/1"="red")
chromUse = sort(chromSizes[isRealChrom], decreasing = TRUE)
for (ch in names(chromUse)){
  par(mar=c(4.1, 12, 4.1, 2.1))
  plot(0, 0, type="n", main=paste("Chromsome", ch), xlab="pos", xlim=c(1, chromSizes[ch]), ylim=c(0, 3*ncol(gt)),
       axes=FALSE, frame=FALSE, xaxs="i", yaxs="i", ylab="")
  axis(1)
  mtext(side = 2, at = seq(1, 3*ncol(gt), by=3), text = colnames(gt), las=2,
        cex = 1.0, font=2, col=sampleColors)
  idx = idxList[[ch]]
  xStart = pos[idx]
  nm  = colnames(gt)[1]
  for (i in 1:ncol(gt)){
    offSet = match(gt[idx ,i], names(snpColors))
    yTop = (i-1) * 3 + offSet
    rect(xStart, yTop - 1, xStart+1, yTop, col = snpColors[offSet], border=snpColors[offSet])
  }
  abline(h=seq(0, 3*ncol(gt), by=3))
}