geneset_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
)

Value

A ggraph (ggplot) object

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.

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