Topological overlap matrix similarity

Source: R/getTOM.R

Calculate TOM by WGCNA

getTOM(
  seu,
  softPower = 2,
  dofilter = TRUE,
  assay = CodexPredefined$defaultAssay,
  output = c("plot", "matrix"),
  hclust_method = "complete",
  ...
)

Arguments

seu

A Seurat object

softPower

Soft thresholding power.

dofilter

logical(1L). Filter the expression data or not.

assay

The expression assay name. Do NOT use GMM.

output

The output of the function. Available options: plot (default), and matrix.

hclust_method

The agglomeration method to be used. See hclust.

...

Parameters for adjacency.

Value

A ggplot object or a dist matrix.