PLNmodels (version 0.9.5)

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

Description

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

Usage

# S3 method for 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 weigth 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

2D numeric. 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 optionaly displays a graph (via igraph or corrplot for large ones)

Examples

# NOT RUN {
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
myNet <- getBestModel(fits)
# }
# NOT RUN {
plot(myNet)
# }