buildPG: buildPG

In WilsonImmunologyLab/LinQView: Integrate information from both transcriptome and cell surface protein signals to better identify cell heterogeneity

Description

build PG based on user's choice (RNA, ADT, Joint or All) MST

Usage

buildPG(object, ...)

Arguments

object	(For default) cell embedding
assay	(For Seurat) user choose the assay data they want to build a MST based on, can be RNA, ADT, Joint or All (All means calculate all three)
mst	(For default) MST for building PG
pg.nodes	parameter for computing Ecipal Graph. number of nodes you want to build PG. if NULL, we will calculated a number based on your data size
pg.min.nodes	parameter for computing Elastic Principal Graph. min value of pg.nodes
pg.Lambda	parameter for computing Elastic Principal Graph, real, the lambda parameter used the compute the elastic energy
pg.Mu	parameter for computing Elastic Principal Graph, real, the lambda parameter used the compute the elastic energy
trimming.radius	parameter for computing Elastic Principal Graph, real, maximal distance of point from a node to affect its embedment
final.energy	parameter for computing Elastic Principal Graph, string indicating the final elastic emergy associated with the configuration. Currently it can be "Base" or "Penalized"
initial.MST	use MST as initial for PG or not. default is FALSE because use MST as initial is time consuming for large dataset

WilsonImmunologyLab/LinQView documentation built on Jan. 3, 2022, 10 p.m.