sbfc_graph {sbfc}

SBFC graph

Description

Plots a sampled MCMC graph or an average of sampled graphs using Graphviz.
In average graphs, nodes are color-coded according to importance - the proportion of samples where the node appeared in Group 1 (dark-shaded nodes appear more often). In average graphs, thickness of edges also corresponds to importance: the proportion of samples where the edge appeared.

Usage

sbfc_graph(
  sbfc_result,
  iter = 10000,
  average = T,
  edge_cutoff = 0.1,
  single_noise_nodes = F,
  labels = paste0("X", 1:ncol(sbfc_result$parents)),
  save_graphviz_code = F,
  colorscheme = "blues",
  ncolors = 7,
  width = NULL,
  height = NULL
)

Arguments

sbfc_result

An object of class sbfc.

iter

MCMC iteration of the sampled graph to plot, if average=F (default=10000).

average

Plot an average of sampled MCMC graphs (default=TRUE).

edge_cutoff

The average graph includes edges that appear in at least this fraction of the sampled graphs, if average=T (default=0.1).

single_noise_nodes

Plot single-node trees that appear in the noise group (Group 0) in at least 80 percent of the samples, which can be numerous for high-dimensional data sets (default=FALSE).

labels

A vector of node labels (default=c("X1","X2",...)).

save_graphviz_code

Save the Graphviz source code in a .gv file (default=FALSE).

colorscheme

Graphviz color scheme for the nodes (default="blues").

ncolors

number of colors in the palette (default=7).

width

An optional parameter for specifying the width of the resulting graphic in pixels.

height

An optional parameter for specifying the height of the resulting graphic in pixels.

Examples

data(madelon)
madelon_result = sbfc(madelon)
sbfc_graph(madelon_result) 
sbfc_graph(madelon_result, average=FALSE, iter=5000) # graph for 5000th iteration
sbfc_graph(madelon_result, single_noise_nodes=TRUE) # wide graph with 480 single nodes

data(heart)
heart_result = sbfc(heart)
heart_labels = c("Age", "Sex", "Chest Pain", "Rest Blood Pressure", "Cholesterol", 
"Blood Sugar", "Rest ECG", "Max Heart Rate", "Angina", "ST Depression", "ST Slope",
"Fluoroscopy Colored Vessels", "Thalassemia")
sbfc_graph(heart_result, labels=heart_labels, width=700)