plotCellNet: Cell network plotting function

In ff98li/scRGNet: Perform scRNA-seq Analysis using Single-cell Graphical Neural Network (scGNN) Framework

Description

A plotting function to plot the inferred cell net-work from generateNetwork.

Usage

plotCellNet(
  net,
  group = TRUE,
  title = "Calculated Cell Network",
  node_size = NULL,
  show_select_by = "none"
)

Arguments

net	An igraph object generayed by generateNetwork. It contains the inferred cell-cell relationship.
group	A logical vector indicating whether to highlight cell communities in the network. If FALSE, they will not be highlighted. Default TRUE.
title	A character vector as the title of the network plot.
node_size	Size of node
show_select_by	Show option to highlight either by "node" or "group". Options: "node" | "group" | "none". Default "none".

References

\insertRef

igraphscRGNet \insertRefvisNetworkscRGNet

Examples

# Example 1:
# Tested examples. Not run for fast package compiling
## Not run: 
# Accessing the demo gene_counts_small dataset available with the package
inputCountsPath <- system.file("extdata", "GSE138852_small.csv", package = "scRGNet")
# Preprocess the raw counts
counts <- preprocessCSV(path = inputCountsPath)
ltmg <- runLTMG(counts)
hyperParams <- setHyperParams(regu_epochs = 5L)
hardwareSetup <- setHardware(coresUsage = 1L)
z <- runFeatureAE(scDataset = counts, LTMG_mat = ltmg, hyperParams, hardwareSetup)
net <- generateNetwork(z)
plotCellNet(net)

## End(Not run)

ff98li/scRGNet documentation built on Jan. 14, 2022, 4:58 a.m.