SSN connectivity plot

generates SSN connectivity plot used to visualize transcriptomic gene network.

SSNExpression(
  cell.object,
  gene.object,
  group_by = "seurat_clusters",
  features = NULL,
  max_cells = 20000,
  connectivity.plot = NULL
)

Arguments

cell.object: Seurat object (gene x cell). Same as input to runSSN(object = cell.object, ...).
gene.object: Seurat object (cell x gene) obtained from SSN analysis.
group_by: meta feature used for grouping. Must be present in `cell.object`.
features: feature to visualize expression.
max_cells: maximum number of cells used. Default is 20000. If number of cells in `cell.object` exceeds `max_cells`, `cell.object` is downsampled.
connecitivity.plot: "plot_edge" generated by SSNConnectivity function. If not specified, not edges are plotted in SSN graph plot.

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

Nicholas Mikolajewicz