plotLog: Log-log plot of Network

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

Description

Generate a A plot of log-frequency against log-rank for the degree distribution. It is useful in examing whether the network has a scale-free topology.

Usage

plotLog(net, title = "A log-log Plot of Connectivities for Cell Network")

Arguments

net	A graph object
title	A string vector as the title of the log-log plot

References

\insertRef

igraphscRGNet \insertRefgraphicsscRGNet

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)
plotLogRank(net)

## End(Not run)

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