collapseGraphPaga: Collapse graph using PAGA 1.2 algorithm, Wolf et al 2019,...
In kharchenkolab/sccore: Core Utilities for Single-Cell RNA-Seq
collapseGraphPaga 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
kharchenkolab/sccore documentation built on Feb. 26, 2024, 12:41 a.m.
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| collapseGraphPaga | 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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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