NIMAA (version 0.2.2)

plotBipartite: Plot the bipartite network and the corresponding projected networks

Description

This function converts the incidence matrix into an igraph object and provides network visualization in multiple ways.

Usage

plotBipartite(
  inc_mat,
  part = 0,
  verbose = FALSE,
  vertex.label.display = FALSE,
  layout = layout.bipartite,
  vertex.shape = c("square", "circle"),
  vertix.color = c("steel blue", "orange"),
  vertex.label.cex = 0.3,
  vertex.size = 4,
  edge.width = 0.4,
  edge.color = "pink"
)

Value

An igraph network object with visualization.

Arguments

inc_mat

A matrix, the incidence matrix of bipartite network.

part

An integer value indicates whether the original bipartite network or its projection should be plotted. The default value of 0 represents the original bipartite network. Other possibilities are 1 and 2 for two projected networks.

verbose

A logical value, if it is TRUE, the plot is saved as the .png file in the working directory. The default value is FALSE.

vertex.label.display

A logical value, if it is TRUE, then the label of each vertex is shown in the output graph. The default value is FALSE.

layout

A function from igraph package. The default is layout.bipartite, so the nodes on the top side are the variables in rows, and the nodes on the bottom side are those in columns.

vertex.shape

A string vector to define the shapes for two different sets of vertices. The default value is c("square", "circle"), the first string value is for the nodes in rows, and the second one is for nodes in columns. If the part is not 0, then only the first string value is used.

vertix.color

A string vector to define the colors for two different sets of vertices. The default value is c("steel blue", "orange"), the first string value is for the nodes in rows, and the second one is for nodes in columns. If the part is not 0, then only the first string value is used.

vertex.label.cex

A numeric value used to define the size of vertex labels. The default value is 0.3.

vertex.size

A numeric value used to define the size of vertex. The default value is 4.

edge.width

A numeric value used to define the edge width. The default value is 0.1.

edge.color

A string used to define the color of edges. The default value is "pink".

Examples

# load part of the beatAML data
beatAML_data <- NIMAA::beatAML[1:10000,]

# convert to incidence matrix
beatAML_incidence_matrix <- nominalAsBinet(beatAML_data)

# plot with the vertex label showing
plotBipartite(inc_mat = beatAML_incidence_matrix, vertex.label.display = TRUE)