SSNExpression: 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

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.

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), SSNConnectivity for connectivity plot.

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