plotOriginalTree: Display Original ctgGEM Plots

Description Usage Arguments Value Note Examples

View source: R/plotOriginalTree.R

Description

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

Usage

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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

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# 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")

bicbioeng/ctgGEM documentation built on July 19, 2020, 12:42 a.m.