rqcFileHeatmap {Rqc} | R Documentation

## 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.

### Author(s)

Welliton Souza

### 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]])

[Package Rqc version 1.16.2 Index]