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.
the ctgGEMset object for creating the cell tree
the type of tree generated
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.
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# 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)
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