plot_graph_lg: Plot graphs

In graph4lg: Build Graphs for Landscape Genetics Analysis

Plot graphs

Description

The function enables to plot graphs, whether spatial or not.

Usage

plot_graph_lg(
  graph,
  crds = NULL,
  mode = "aspatial",
  node_inter = NULL,
  link_width = NULL,
  node_size = NULL,
  module = NULL,
  pts_col = NULL
)

Arguments

graph	A graph object of class igraph
crds	(optional, default = NULL) If 'mode = 'spatial”, it is a data.frame with the spatial coordinates of the graph nodes. It must have three columns : ID: A character string indicating the name of the graph nodes. The names must be the same as the node names of the graph of class igraph (igraph::V(graph)$name) x: A numeric or integer indicating the longitude of the graph nodes. y: A numeric or integer indicating the latitude of the graph nodes. This argument is not used when 'mode = 'aspatial” and mandatory when 'mode = 'spatial”.
mode	A character string indicating whether the graph is spatial ('mode = 'spatial”) or not ('mode = 'aspatial” (default))
node_inter	(optional, default = NULL) A character string indicating whether the links of the graph are weighted by distances or by similarity indices. It is only used when 'mode = 'aspatial” to compute the node positions with Fruchterman and Reingold algorithm. It can be equal to: 'distance': Link weights correspond to distances. Nodes that are close to each other will be close on the figure. 'similarity': Link weights correspond to similarity indices. Nodes that are similar to each other will be close on the figure.
link_width	(optional, default = NULL) A character string indicating how the width of the link is set on the figure. Their width can be: inversely proportional to link weights ("inv_w", convenient with distances, default) proportional to link weights ("w")
node_size	(optional, default = NULL) A character string indicating the graph node attribute used to set the node size on the figure. It must be the name of a numeric or integer node attribute from the graph.
module	(optional, default = NULL) A character string indicating the graph node modules used to set the node color on the figure. It must be the name of a node attribute from the graph with discrete values.
pts_col	(optional, default = NULL) A character string indicating the color used to plot the nodes (default: "#F2B950"). It must be a hexadecimal color code or a color used by default in R. It cannot be used if 'module' is specified.

Details

When the graph is not spatial ('mode = 'aspatial”), the nodes coordinates are calculated with Fruchterman et Reingold algorithm. The graph object graph of class igraph must have node names (not necessarily in the same order as IDs in crds, given a merging is done).

Value

A ggplot2 object to plot

Author(s)

P. Savary

References

\insertRef

fruchterman1991graphgraph4lg

Examples

data(pts_pop_ex)
data(data_ex_genind)
mat_w <- mat_gen_dist(data_ex_genind, dist = "DPS")
gp <- gen_graph_topo(mat_w = mat_w, topo = "mst")
g <- plot_graph_lg(graph = gp,
                             crds = pts_pop_ex,
                             mode = "spatial",
                             link_width = "inv_w")

graph4lg documentation built on Feb. 16, 2023, 5:43 p.m.