convertToEnrichedHeatmapMat: export a profileplyr object to a list of matrices that can be...

In RockefellerUniversity/profileplyr: Visualization and annotation of read signal over genomic ranges with profileplyr

export a profileplyr object to a list of matrices that can be used as an input for EnrichedHeatmap

Description

export a profileplyr object to a list of matrices that can be used as an input for EnrichedHeatmap

Usage

convertToEnrichedHeatmapMat(object = "profileplyr", sample_names = "character")

## S4 method for signature 'profileplyr'
convertToEnrichedHeatmapMat(object = "profileplyr", sample_names = NULL)

Arguments

object	A profileplyr object
sample_names	A character vector that will set the names of the heatmap components that are generated from the profileplyr assays() matrices. This argument is optional, by default the names will be the name of the samples in the profileplyr object rownames(sampleData(object)).

Details

Takes a profileplyr object and converts all of the matrices in the assays() section of the object to matrices that can be used as an input for EnrichedHeatmap

Value

A list of normalized matrices that can be used for generating visualizations with EnrichedHeatmap

Methods (by class)

• convertToEnrichedHeatmapMat(profileplyr): export a profileplyr object to a list of matrices that can be used as an input for EnrichedHeatmap

Examples

example <- system.file("extdata", "example_deepTools_MAT", package = "profileplyr") 
object <- import_deepToolsMat(example) 

library(EnrichedHeatmap)
EH_mat <- convertToEnrichedHeatmapMat(object)
EnrichedHeatmap(EH_mat[[1]], name = names(EH_mat[1]), column_title = names(EH_mat[1]))

RockefellerUniversity/profileplyr documentation built on Jan. 28, 2023, 10:09 a.m.