SSN connectivity plot

generates SSN connectivity plot used to visualize transcriptomic gene network.

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.

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)

Author

Nicholas Mikolajewicz