plot.PLNnetworkfit: Extract and plot the network (partial correlation, support or...

In PLN-team/PLNmodels: Poisson Lognormal Models

Extract and plot the network (partial correlation, support or inverse covariance) from a PLNnetworkfit object

Description

Extract and plot the network (partial correlation, support or inverse covariance) from a PLNnetworkfit object

Usage

## S3 method for class 'PLNnetworkfit'
plot(
  x,
  type = c("partial_cor", "support"),
  output = c("igraph", "corrplot"),
  edge.color = c("#F8766D", "#00BFC4"),
  remove.isolated = FALSE,
  node.labels = NULL,
  layout = layout_in_circle,
  plot = TRUE,
  ...
)

Arguments

x	an R6 object with class PLNnetworkfit
type	character. Value of the weight of the edges in the network, either "partial_cor" (partial correlation) or "support" (binary). Default is "partial_cor".
output	the type of output used: either 'igraph' or 'corrplot'. Default is 'igraph'.
edge.color	Length 2 color vector. Color for positive/negative edges. Default is c("#F8766D", "#00BFC4"). Only relevant for igraph output.
remove.isolated	if TRUE, isolated node are remove before plotting. Only relevant for igraph output.
node.labels	vector of character. The labels of the nodes. The default will use the column names ot the response matrix.
layout	an optional igraph layout. Only relevant for igraph output.
plot	logical. Should the final network be displayed or only sent back to the user. Default is TRUE.
...	Not used (S3 compatibility).

Value

Send back an invisible object (igraph or Matrix, depending on the output chosen) and optionally displays a graph (via igraph or corrplot for large ones)

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
myNet <- getBestModel(fits)
## Not run: 
plot(myNet)

## End(Not run)

PLN-team/PLNmodels documentation built on Oct. 13, 2024, 4:01 a.m.