springNet: Generate spring-embedded network from similarity matrix

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Generate spring-embedded network from similarity matrix

Description

Generate spring-embedded network from similarity matrix

Usage

springNet(
  smat,
  layout = "nicely",
  group_by = NULL,
  cex_line = 0.1,
  knn = 5,
  min_edge = quantile(smat, 0.95),
  dual_criteria = F,
  node_label_size = NULL,
  node_size = 1,
  label_as_node = F,
  remove_unconnected_nodes = F,
  seed = 1023
)

Arguments

smat	similarity matrix
layout	layout used to embded network. Default is "nicely",
group_by	group variable used to color network nodes
cex_line	edge width
knn	k-nearest neighbors. Default is 5. If not specified, defaults to min_edge argument.
min_edge	similarity threshold used to display network edge
dual_criteria	if knn and min_edge are both specified, edges are included if either condition are met.
node_label_size	size of node labels. If not specified (i.e., node_label_size = NULL), no label is shown.
node_size	size of network nodes. Default is 1.
label_as_node	replace nodes with labels. Default is F.
remove_unconnected_nodes	remove unconnected nodes in graph. Default is F.
seed	number used to initialize pseudorandom number generator. Specify to ensure reproducible graphs. Default is 1023.

Value

ggplot

Author(s)

Nicholas Mikolajewicz

Examples

smat <- cor(x)
springNet(smat)

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.