geneset_topology: geneset_topology

In SiFINeT: Single Cell Feature Identification with Network Topology

geneset_topology

Description

The function plots the topology network of the feature gene sets found by SiFINeT.

Usage

geneset_topology(
  so,
  weightthres = 0.3,
  edge_method = 2,
  node_color = "black",
  shiftsize = 0.05,
  boundsize = 0.3,
  prefix = "",
  set_name = NULL
)

Arguments

so	a SiFINeT object
weightthres	edges between nodes (feature gene sets) with weight greater than weightthres would be shown in the plot
edge_method	SiFINeT provides 2 methods of calculating edge weight. The number of shared feature genes between feature gene sets would be used when edge_method = 1; while the edge proportion between feature gene sets would be applied if edge_method = 2.
node_color	color of nodes. Should have either length 1 or same length as the number of feature gene sets.
shiftsize	set the distance between center of label and the corresponding feature gene sets node.
boundsize	set the size of the boundary region.
prefix	the prefix of the labels
set_name	name of the gene sets

Details

This function visualizes the output feature gene sets of SiFINeT in the form of network. Number of shared feature genes or proportion of edges between feature gene sets could be used to weight the edges. The layout of the nodes is created by create_layout function in ggraph package.

Value

A ggraph (ggplot) object

References

Thomas Lin Pedersen (2022). ggraph: An Implementation of Grammar of Graphics for Graphs and Networks. R package version 2.0.6. https://CRAN.R-project.org/package=ggraph

SiFINeT documentation built on April 3, 2025, 9:30 p.m.