| getExtraneousCladeSubpopulations {PAC} | R Documentation |
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
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.
Usage
getExtraneousCladeSubpopulations(tsneResults, pacman_results,
threshold_multiplier, max_threshold)
Arguments
tsneResults |
t-SNE output of clade centroids' embedding. |
pacman_results |
PAC-MAN analysis result matrix that contains network annotation, clade IDs and mean (centroid) clade expression levels. |
threshold_multiplier |
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). |
max_threshold |
the maximum distance (on t-SNE plane) allowed for sample subpopulations to be categorized into the same clade. |
Value
Returns clade subpopulations to be pruned.