format_fortify: format_fortify
In phyloseqGraphTest: Graph-Based Permutation Tests for Microbiome Data

format_fortify

R Documentation

format_fortify

Description

a unified function to format network or igraph object. Copied with very slight modification from https://github.com/briatte/ggnetwork/blob/master/R/utilities.R to fix the same CRAN problem as new_fortify.igraph.

Usage

format_fortify(
  model,
  nodes = NULL,
  weights = NULL,
  arrow.gap = 0,
  by = NULL,
  scale = TRUE,
  stringsAsFactors = getOption("stringsAsFactors", FALSE),
  .list_vertex_attributes_fun = NULL,
  .get_vertex_attributes_fun = NULL,
  .list_edges_attributes_fun = NULL,
  .get_edges_attributes_fun = NULL,
  .as_edges_list_fun = NULL
)

Arguments

`model`	an object of class `network` or `igraph`.
`nodes`	a nodes object from a call to fortify.
`weights`	the name of an edge attribute to use as edge weights when computing the network layout, if the layout supports such weights (see 'Details'). Defaults to `NULL` (no edge weights).
`arrow.gap`	a parameter that will shorten the network edges in order to avoid overplotting edge arrows and nodes; defaults to `0` when the network is undirected (no edge shortening), or to `0.025` when the network is directed. Small values near `0.025` will generally achieve good results when the size of the nodes is reasonably small.
`by`	a character vector that matches an edge attribute, which will be used to generate a data frame that can be plotted with `facet_wrap` or `facet_grid`. The nodes of the network will appear in all facets, at the same coordinates. Defaults to `NULL` (no faceting).
`scale`	whether to (re)scale the layout coordinates. Defaults to `TRUE`, but should be set to `FALSE` if `layout` contains meaningful spatial coordinates, such as latitude and longitude.
`stringsAsFactors`	whether vertex and edge attributes should be converted to factors if they are of class `character`. Defaults to the value of `getOption("stringsAsFactors")`, which is `FALSE` by default: see `data.frame`.
`.list_vertex_attributes_fun`	a "list vertex attributes" function.
`.get_vertex_attributes_fun`	a "get vertex attributes" function.
`.list_edges_attributes_fun`	a "get edges attributes" function.
`.get_edges_attributes_fun`	a "get edges attributes" function.
`.as_edges_list_fun`	a "as edges list" function.