plotOriginalTree: Display Original ctgGEM Plots

In ctgGEM: Generating Tree Hierarchy Visualizations from Gene Expression Data

Description

Displays the original plots created by the ctgGEM package and stored in the originalTrees slot of a ctgGEMset object.

Usage

plotOriginalTree(dataSet, treeType)

Arguments

dataSet	a ctgGEMset object
treeType	the type of tree to display. Must be one of names(originalTrees(dataSet))

Value

For treeType = "destinyDM" and treeType = "destinyDPT", returns NULL. For all other tree types, a ggplot2::ggplot object.

Note

In order to reproduce original oncoNEM trees or destiny plots, the respective package(s) must be installed.

Examples

# load HSMMSingleCell package
library(HSMMSingleCell)

# load the data for TSCAN and monocle:
data(HSMM_expr_matrix)
data(HSMM_sample_sheet)
data(HSMM_gene_annotation)

# construct a ctgGEMset
dataSet <- ctgGEMset(exprsData = HSMM_expr_matrix,
                        phenoData = HSMM_sample_sheet,
                        featureData = HSMM_gene_annotation)

TSCANinfo(dataSet) <- "ENSG00000000003.10"

# run generate_tree()
dataSet <- generate_tree(dataSet = dataSet, treeType = "TSCAN")

# view names of original trees
names(originalTrees(dataSet))

# plot original trees
plotOriginalTree(dataSet, "TSCANclustering")
plotOriginalTree(dataSet, "TSCANsingleGene")

ctgGEM documentation built on Nov. 8, 2020, 5:54 p.m.