| generate_tree {ctgGEM} | R Documentation |
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.
generate_tree(dataSet, treeType, outputDir = NULL)
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 |
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.
# 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)