plot_vr_graph {TDApplied}

Plot a VR graph using the igraph package.

Description

This function will throw an error if the igraph package is not installed.

Usage

plot_vr_graph(
  graphs,
  eps,
  cols = NULL,
  layout = NULL,
  title = NULL,
  component_of = NULL,
  plot_isolated_vertices = FALSE,
  return_layout = FALSE,
  vertex_labels = TRUE
)

Arguments

graphs

the output of a 'vr_graphs' function call.

eps

the numeric radius of the graph in 'graphs' to plot.

cols

an optional character vector of vertex colors, default 'NULL'.

layout

an optional 2D matrix of vertex coordinates, default 'NULL'. If row names are supplied they can be used to subset a graph by those vertex names.

title

an optional str title for the plot, default 'NULL'.

component_of

a vertex name (integer or character), only the component of the graph containing that vertex will be plotted (useful for identifying representative (co)cycles in graphs). Default 'NULL' (plot the whole graph).

plot_isolated_vertices

a boolean representing whether or not to plot isolated vertices, default 'FALSE'.

return_layout

a boolean representing whether or not to return the plotting layout (x-y coordinates of each vertex) and the vertex labels, default 'FALSE'.

vertex_labels

a boolean representing whether or not to plot vertex labels, default 'TRUE'.

Value

if 'return_layout' is 'TRUE' then a list with elements "layout" (the numeric matrix of vertex x-y coordinates) and "vertices" (character vertex labels), otherwise the function does not return anything.

Author(s)

Shael Brown - [e-mail]

See Also

vr_graphs for computing VR graphs.

Examples

if(require("TDAstats") & require("igraph"))
{
  # simulate data from the unit circle and calculate 
  # its diagram
  df <- TDAstats::circle2d[sample(1:100,25),]
  diag <- TDAstats::calculate_homology(df,
                                       dim = 1,
                                       threshold = 2)
  
  # get minimum death radius of any data cluster
  min_death_H0 <- 
  min(diag[which(diag[,1] == 0),3L])
  
  # get birth and death radius of the loop
  loop_birth <- as.numeric(diag[nrow(diag),2L])
  loop_death <- as.numeric(diag[nrow(diag),3L])

  # compute VR graphs at radii half of 
  # min_death_H0 and the mean of loop_birth and 
  # loop_death, returning clusters
  graphs <- vr_graphs(X = df,eps = 
  c(0.5*min_death_H0,(loop_birth + loop_death)/2))
  
  # plot graph of smaller (first) radius
  plot_vr_graph(graphs = graphs,eps = 0.5*min_death_H0,
                  plot_isolated_vertices = TRUE)
  
  # plot graph of larger (second) radius
  plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2)
  
  # repeat but with rownames for df, each vertex
  # will be plotted with its rownames
  rownames(df) <- paste0("V",1:25)
  graphs <- vr_graphs(X = df,eps = 
  c(0.5*min_death_H0,(loop_birth + loop_death)/2))
  plot_vr_graph(graphs = graphs,eps = 0.5*min_death_H0,
                  plot_isolated_vertices = TRUE)
  
  # plot without vertex labels
  plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2,
                  vertex_labels = FALSE)
                 
  # plot only the graph component containing vertex "1"
  plot_vr_graph(graphs = graphs,eps = 0.5*min_death_H0,
                  component_of = "V1",plot_isolated_vertices = TRUE)
 
  # save the layout of the graph for adding features to 
  # the same graph layout, like color
  layout <- plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2,
                            return_layout = TRUE,vertex_labels = TRUE)
  cols <- rep("blue",25)
  cols[1:5] <- "red"
  plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2,cols = cols,
                  layout = layout)
  
}