Rqc (version 1.6.2)

rqcFileHeatmap: Heatmap of distance matrix of top over-represented reads

Description

This function plots a heatmap of distance matrix of top over-represented reads. This function does not work with list of RqcResultSet objects, only with one RqcResultSet object.

Usage

rqcFileHeatmap(rqcResultSet, dist.method = "euclidean", hclust.method = "ward.D")

Arguments

rqcResultSet

RqcResultSet object created by rqc and rqcQA functions.

dist.method

the distance measure to be used by dist function.

hclust.method

the agglomeration method to be used by hclust function.

Value

Plot object from ggplot function.

Examples

checkpoint("Rqc", path=system.file(package="Rqc", "extdata"), {
  folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
  files <- list.files(full.names=TRUE, path=folder)
  rqcResultSet <- rqcQA(files, pair=c(1,1), workers=1)
}, keep="rqcResultSet")
rqcFileHeatmap(rqcResultSet[[1]])