R: Collapse graph using PAGA 1.2 algorithm, Wolf et al 2019,...

collapseGraphPaga {sccore} | R Documentation

## 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

[Package sccore version 1.0.1 Index]