Distances: Calculate Summary Statistics

In tallulandrews/TreeOfCells: Inferring the Tree of Cells

Description

Calculates summary statistics to facilitate the fitting of a ZINB model, performs various data input checks.

Usage

	base_dist(merged_profiles, type="euclidean")
	pearson_dist(merged_profiles, type="pearson")
	spearman_dist(merged_profiles, type="spearman")
	phis_dist(merged_profiles)
	rhop_dist(merged_profiles)
	cosine_dist(merged_profiles)

Arguments

merged_profiles	Output from: merge_profiles function.
type	type of distance to calcuate for methods with multiple options.

Details

Calculates all pairwise distances between cell-types, using different distance measures. base_dist = wrapper of stats::dist methods pearson_dist/spearman_dist = 1 - correlation, wrapper of stats::cor methods. phis_dist = wrapper of propr::phis. rhop_dist = 1 - propr::perb. cosine_dist = 1 - lsa::cosine.

For phis and rhop proportion methods, profiles are shifted up so that none of the values are negative.

Value

Distance matrix.

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))
d1 <- base_dist(obj, type="manhattan")
d2 <- spearman_dist(obj)
d3 <- pearson_dist(obj)
d4 <- phis_dist(obj)
d5 <- rhop_dist(obj)
d6 <- cosine_dist(obj)

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