plotNetwork: Plot Feature Network

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Plot Feature Network

Description

Plot Feature Network

Usage

plotNetwork(
  dataset = NULL,
  factor = NULL,
  rank = NULL,
  fts = NULL,
  method = c("se.mb", "se.glasso"),
  format = c("ggplot", "igraph"),
  fill = NULL,
  outline = NULL,
  labelfts = NULL,
  labelAll = F,
  deg_cutoff = 0,
  r_cutoff = 0,
  top_r_prop = 100,
  layout = c("fr", "circle", "sphere", "dh", "nicely")
)

Arguments

dataset	MicroVis dataset. Defaults to the active dataset
factor	(Optional) Factor to split data along groups
rank	Rank at which to build network
fts	List of specific features to analyze and plot
method	Co-occurence analysis method
format	Use ggplot or igraph to plot the network?
fill	How node colors are chosen
outline	(Optional) How node outlines are chosen, if at all. Defaults to no outline
labelfts	Which nodes are labeled, if any. Defaults to none
labelAll	Label all features in the network? Defaults to FALSE
deg_cutoff	Only display nodes with at least this many connections/edges. Defaults to 0
r_cutoff	Only display connections/edges with an absolute value of this or more
top_r_prop	Only display the top percentile of connections by absolute value
layout	Layout for nodes

Value

Network plot

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.