getExtraneousCladeSubpopulations

t-SNE output of clade centroids' embedding.

tsneResults

PAC-MAN analysis result matrix that contains network annotation, clade IDs and mean (centroid) clade expression levels.

pacman_results

how many times the threshold ( (a) spread from center of clade for clades with three or more sample subpopulations and (b) distance from each subpopulation centroid for clades with exactly two subpopulations).

threshold_multiplier

the maximum distance (on t-SNE plane) allowed for sample subpopulations to be categorized into the same clade.

max_threshold

Calculates subpopulations in clades (with two or more subpopulations) that are too far away from other subpopulations (within the same clade) on the constellation plot; these far away subpopulations should be pruned away from the original clades.

Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) <doi:10.1371/journal.pcbi.1005875> for detail method description.

Ye Li

Partition-Assisted Clustering and Multiple Alignments of
Networks

getExtraneousCladeSubpopulations function

Calculates subpopulations in clades (with two or more subpopulations) that are too far away from other subpopulations (within the same clade) on the constellation plot; these far away subpopulations should be pruned away from the original clades. — getExtraneousCladeSubpopulations

Calculates subpopulations in clades (with two or more subpopulations) that are too far away from other subpopulations (within the same clade) on the constellation plot; these far away subpopulations should be pruned away from the original clades.

getExtraneousCladeSubpopulations: Calculates subpopulations in clades (with two or more subpopulations) that are too far away from other subpopulations (within the same clade) on the constellation plot; these far away subpopulations should be pruned away from the original clades.

Description

Usage

Arguments

Value