ctgPHYLset-methods: Methods for the ctgPHYLset class

In bicbioeng/ctgPHYL: Package for Single-cell Data Visualization and Analysis

Description

These methods operate on ctgPHYLset objects. Please note that treeList<- and originalTrees<- are not exported and not intended to be called directly.

Usage

cellscapeData(cs, pt = NULL)

cellscapeData(cs, pt) <- value

timescapeData(cs, pt = NULL)

timescapeData(cs, pt) <- value

mapscapeData(cs, pt = NULL)

mapscapeData(cs, pt) <- value

treeList(cs)

treeList(cs, tt) <- value

originalTrees(cs)

originalTrees(cs, tt) <- value

Arguments

cs	A ctgPHYLset object
pt	The name of the cellscape, timescape, or mapscape parameter to store
value	cellscapeData(cs, pt)<-: The value to use as a named parameter for cellscape, used by generate_tree(treeType = "cellscape") in the cellTreeGenerator workflow timescapeData(cs, pt)<-: The value to use as a named parameter for timescape used by generate_tree(treeType = "timescape") in the cellTreeGenerator workflow mapscapeData(cs)<-: The value to use as a named parameter for mapscape, used by generate_tree(treeType = "mapscape") in the cellTreeGenerator workflow
tt	The type of tree being stored

Value

An updated ctgPHYLset object, or the contents of a slot of the ctgPHYLset object

Examples

# load data for 'treeType = cellscape'
cs_tree_edges <- read.csv(system.file("extdata", "cnv_tree_edges.csv",
                         package = "cellscape"))
cs_cnv_data <- read.csv(system.file("extdata", "cnv_data.csv",
                                     package = "cellscape"))
cs_sc_annot <- read.csv(system.file("extdata", "cnv_annots.tsv",
                                    package = "cellscape"), sep="\t")
cs_clone_colours <- data.frame(clone_id = c("1","2","3"),
                               colour = c("7fc97f", "beaed4", "fdc086"))

# create example ctgPHYLset and load data into it
ctgPHYLset <- ctgPHYLset()
cellscapeData(ctgPHYLset, "clone_colours") <- cs_clone_colours
cellscapeData(ctgPHYLset, "tree_edges") <- cs_tree_edges
cellscapeData(ctgPHYLset, "cnv_data") <- cs_cnv_data
cellscapeData(ctgPHYLset, "sc_annot") <- cs_sc_annot

# run generate_tree()
ctgPHYLset <- generate_tree(dataSet = ctgPHYLset, treeType = "cellscape")

trees <- treeList(ctgPHYLset)
originalTrees <- originalTrees(ctgPHYLset)

bicbioeng/ctgPHYL documentation built on April 13, 2020, 12:38 a.m.