collapseGraphPaga {sccore}

Collapse graph using PAGA 1.2 algorithm, Wolf et al 2019, Genome Biology (2019) <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1663-x>

Description

Collapse graph using PAGA 1.2 algorithm, Wolf et al 2019, Genome Biology (2019) <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1663-x>

Usage

collapseGraphPaga(graph, groups, linearize = TRUE, winsorize = FALSE)

Arguments

graph

igraph graph object Graph to be collapsed

groups

factor on vertices describing cluster assignment (can specify integer vertex ids, or character vertex names which will be matched)

linearize

should normally be always TRUE (default=TRUE)

winsorize

winsorize final connectivity statistics value (default=FALSE) Note: Original PAGA has it as always TRUE, but in this case there is no way to distinguish level of connectivity for highly connected groups.

Value

collapsed graph