plotOriginalTree {ctgGEM} | R Documentation

## Display Original ctgGEM Plots

### Description

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

### Usage

    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 `treeType = "cellTreeTopics"` or `"cellTreeGrouping"`, an igraph object. 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

    # load HSMMSingleCell package
    library(HSMMSingleCell)

    # load the data for cellTree, 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")

[Package ctgGEM version 0.99.3 Index]