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

plot.PLNnetworkfit {PLNmodels} | R Documentation

## 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)

[Package PLNmodels version 0.11.6 Index]