tree_of_cells: Build Tree of Cells

In tallulandrews/TreeOfCells: Inferring the Tree of Cells

Description

Calculates cell-type x cell-type distance matrix then builds the tree of cell using a neighbour joining algorithm.

Usage

tree_of_cells( merged_profiles, gene_features=rownames(merged_profiles$mus), dist_func=pearson_dist, plot_type="radial")

Arguments

merged_profiles	Output from: merge_profiles function.
gene_features	genes to use
dist_func	distance function for cell-type distances.
plot_type	how to plot the final tree.

Details

Takes a set of merged profiles for a large number of cell types and calculated cell-type x cell-type distances using the specified distance function and the specified feature genes. This distance matrix is then used as input to the neighbour joining algorithm (from phangorn package) to build a tree of cell-types.

Value

list containing the pair-wise distance matrix and the tree object.

Examples

obj <- list(
	mus = matrix(rnorm(200), ncol=10),
	rs  = matrix(rgamma(200, shape=0.75, scale=1), ncol=10),
	ds  = matrix(runif(200), ncol=10),
	Ns  = matrix(rpois(200, lambda=30), ncol=10))
colnames(obj$mus) <- paste("celltype", 1:ncol(obj$mus), sep="")
rownames(obj$mus) <- paste("gene", 1:nrow(obj$mus), sep="")
colnames(obj$rs) <- paste("celltype", 1:ncol(obj$mus), sep="")
colnames(obj$ds) <- paste("celltype", 1:ncol(obj$mus), sep="")
colnames(obj$Ns) <- paste("celltype", 1:ncol(obj$mus), sep="")
out <- tree_of_cells(obj);

tallulandrews/TreeOfCells documentation built on April 26, 2020, 2:43 p.m.