SSNConnectivity: SSN connectivity plot

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

SSN connectivity plot

Description

generates SSN connectivity plot used to visualize transcriptomic gene network.

Usage

SSNConnectivity(
  gene.object,
  gene.list = NULL,
  quantile_threshold = 0.9,
  raster_dpi = 200,
  edge.alpha = 0.015,
  edge.color = "black",
  node.color = "grey",
  node.alpha = 1,
  node.weights = F,
  node.size.min = 1,
  node.size.max = 5,
  do.label = T,
  label.size = 5,
  verbose = T
)

Arguments

gene.object	Seurat object (cell x gene) obtained from SSN analysis.
gene.list	named list of gene program features/genes. If omitted, feature-annotated connectivity plot is not generated.
quantile_threshold	Quantile threshold for visualized SSN graph edges. Default is 0.9.
raster_dpi	prefix added to each named entry in list. Default is "".
edge.alpha	alpha [0,1] parameter (i.e., transparency) for network edges. Default is 0.015. Use larger values for less dense networks.
edge.color	color of network edges. Default is 'black'.
node.color	color of node edges. Default is 'grey'.
node.alpha	alpha [0,1] parameter for nodes. Default is 1 (obaque).
node.weights	scale node size by connectivity weights. Default is F.
node.size.min	minimal node size. Ignored if node.weights = F. Default is 1.
node.size.max	maximal node size. Ignored if node.weights = F. Default is 5.
do.label	Show gene program IDs on network graph. Default is T.
label.size	Size of gene program IDs on network graph. Default is 5.
verbose	Print progress. Default is T.

Value

Returns 2 variants of SSN connectivity plot along with data.frame used to generate plots.

Author(s)

Nicholas Mikolajewicz

References

https://nmikolajewicz.github.io/scMiko/articles/Module_Detection.html

See Also

runSSN for SSN analysis (gene.object), pruneSSN for gene program features (gene.list)

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