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)