PerformNetworkCorrelation: Function to call for correlation network

In xia-lab/MicrobiomeAnalystR: MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.

Function to call for correlation network

Description

This function runs the fastspar or cor.test

Usage

PerformNetworkCorrelation(
  mbSetObj,
  taxrank,
  cor.method = "pearson",
  colorOpt = "expr",
  permNum = 100,
  pvalCutoff = 0.05,
  corrCutoff = 0.3,
  abundOpt = "mean",
  corr.net.name,
  plotNet = FALSE,
  netType = "static",
  netLayout = "kk",
  netTextSize = 2.5
)

Arguments

mbSetObj	Input the name of the mbSetObj.
taxrank	Character, input the taxonomic level to perform partial correlation analysis.
cor.method	Character, input the correlation method. Supported methods are pearson, spearman, kendall and sparcc.
colorOpt	Character, input what to color the nodes by. Default the nodes will be colored by their expression levels.
permNum	Numeric, input the number of permutations to perform. Default is set to 100.
pvalCutoff	Numeric, input the p-value cutoff. Default is set to 0.05.
corrCutoff	Numeric, input the correlation cutoff. Default is set to 0.3.
abundOpt	Character, default is set to "mean".
corr.net.name	Character, input the name of the plot to save.
plotNet	Boolean. Set to TRUE if you would like a network visualization outputted to your current working directory.
netLayout	Character, layout from ggraph. "kk" for the spring-based algorithm by Kamada and Kawai as default. "drl" for force directed algorithm from the DrL toolbox. "lgl" for Large Graph Layout. "fr" for force-directed of Fruchterman and Reingold.
netTextSize	Numeric, input the preferred font size to be used in the network plot.
networkType	Character, "static" to create a static image or "interactive" to create an interactive network saved as an html in your working directory.

xia-lab/MicrobiomeAnalystR documentation built on April 17, 2024, 7:45 p.m.