generate_tree: Function to Generate Cell Trees

In bicbioeng/ctgGEM: Generating Tree Hierarchy Visualizations from Gene Expression Data

Description

This function builds a cell hierarchy tree of a chosen supported type with a given data set, contained in a ctgGEMset object. Different tree types require data from corresponding slots of the ctgGEMset object. See vignette for examples, usage details, and instructions on building a ctgGEMset object.

Usage

generate_tree(dataSet, treeType, outputDir = NULL)

Arguments

dataSet	the ctgGEMset object for creating the cell tree
treeType	the type of tree generated
outputDir	the directory where output should be saved, defaults to the temporary location returned by tempdir()

Value

An updated ctgGEMset object. The generated tree is placed in @treeList[treeType] slot, and can be accessed via treeList(dataSet)$treeType. The function also creates a directory named "treeType-Output" and writes the plot(s) of the generated tree(s) and its SIF file to that directory.

Examples

# load HSMMSingleCell package
library(HSMMSingleCell)

# load the data
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"

# choose output directory
od <- getwd()
# run generate_tree()
dataSet <- generate_tree(dataSet = dataSet, treeType = "TSCAN",
                         outputDir = od)

bicbioeng/ctgGEM documentation built on Sept. 5, 2021, 8:42 p.m.