Centrality-based network visualization

This function has been developed for the visualization of a network based on applying a centrality measure to the size and color of network nodes. You are also able to adjust the directedness and weight of connections. Some of the documentations of the arguments of this function have been adapted from ggplot2 and igraph packages. A shiny app has also been developed for the calculation of IVI as well as IVI-based network visualization, which is accessible using the `influential::runShinyApp("IVI")` command. You can also access the shiny app online at https://influential.erc.monash.edu/.

Usage

cent_network.vis(
  graph,
  cent.metric,
  layout = "kk",
  node.group = NULL,
  node.color = "viridis",
  node.size.min = 3,
  node.size.max = 15,
  dist.power = 1,
  node.shape = "circle",
  stroke.size = 1.5,
  stroke.color = "identical",
  stroke.alpha = 0.6,
  show.labels = TRUE,
  label.cex = 0.4,
  label.color = "black",
  directed = FALSE,
  arrow.width = 25,
  arrow.length = 0.07,
  edge.width = 0.5,
  weighted = FALSE,
  edge.width.min = 0.2,
  edge.width.max = 1,
  edge.color = "grey75",
  edge.linetype = "solid",
  legend.position = "right",
  legend.direction = "vertical",
  legend.title = "Centrality\nmeasure",
  boxed.legend = TRUE,
  show.plot.title = TRUE,
  plot.title = "Centrality Measure-based Network",
  title.position = "center",
  show.bottom.border = TRUE,
  show.left.border = TRUE,
  seed = 1234
)

Arguments

graph: A graph (network) of the igraph class.
cent.metric: A numeric vector of the desired centrality measure previously calculated by any means. For example, you may use the function ivi for the calculation of the Integrated Value of Influence (IVI) of network nodes. Please note that if the centrality measure has been calculated by any means other than the influential package, make sure that the order of the values in the cent.metric vector is consistent with the order of vertices in the network (V(graph)).
layout: The layout to be used for organizing network nodes. Current available layouts include "kk", "star", "tree", "components", "circle", "automatic", "grid", "sphere", "random", "dh", "drl", "fr", "gem", "graphopt", "lgl", "mds", and "sugiyama" (default is set to "kk"). For a complete description of different layouts and their underlying algorithms please refer to the function layout_.
node.group: A vector of the same length as the number of network nodes defining the group each node of the network belongs to.
node.color: A character string indicating the colormap option to use. Five options are available: "magma" (or "A"), "inferno" (or "B"), "plasma" (or "C"), "viridis" (or "D", the default option) and "cividis" (or "E").
node.size.min: The size of nodes with the lowest value of the centrality measure (default is set to 3).
node.size.max: The size of nodes with the highest value of the centrality measure (default is set to 15).
dist.power: The power to be used to visualize more distinction between nodes with high and low centrality measure values. The higher the power, the smaller the nodes with lower values of the centrality measure will become. Default is set to 1, meaning the relative sizes of nodes are reflective of their actual centrality measure values.
node.shape: The shape of nodes. Current available shapes include "circle", "square", "diamond", "triangle", and "inverted triangle" (default is set to "circle"). You can also set different shapes to different groups of nodes by providing a character vector of shapes of nodes with the same length and order of network vertices. This is useful when plotting a network that include different type of node (for example, up- and down-regulated features).
stroke.size: The size of stroke (border) around the nodes (default is set to 1.5).
stroke.color: The color of stroke (border) around the nodes (default is set to "identical" meaning that the stroke color of a node will be identical to its corresponding node color). You can also set different colors to different groups of nodes by providing a character vector of colors of nodes with the same length and order of network vertices. This is useful when plotting a network that include different type of node (for example, up- and down-regulated features).
stroke.alpha: The transparency of the stroke (border) around the nodes which should be a number between 0 and 1 (default is set to 0.6).
show.labels: Logical scalar, whether to show node labels or not (default is set to TRUE).
label.cex: The amount by which node labels should be scaled relative to the node sizes (default is set to 0.4).
label.color: The color of node labels (default is set to "black").
directed: Logical scalar, whether to draw the network as directed or not (default is set to FALSE).
arrow.width: The width of arrows in the case the network is directed (default is set to 25).
arrow.length: The length of arrows in inch in the case the network is directed (default is set to 0.07).
edge.width: The constant width of edges if the network is unweighted (default is set to 0.5).
weighted: Logical scalar, whether the network is a weighted network or not (default is set to FALSE).
edge.width.min: The width of edges with the lowest weight (default is set to 0.2). This parameter is ignored for unweighted networks.
edge.width.max: The width of edges with the highest weight (default is set to 1). This parameter is ignored for unweighted networks.
edge.color: The color of edges (default is set to "grey75").
edge.linetype: The line type of edges. Current available linetypes include "twodash", "longdash", "dotdash", "dotted", "dashed", and "solid" (default is set to "solid").
legend.position: The position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector). The default is set to "right".
legend.direction: layout of items in legends ("horizontal" or "vertical"). The default is set to "vertical".
legend.title: The legend title in the string format (default is set to "Centrality measure").
boxed.legend: Logical scalar, whether to draw a box around the legend or not (default is set to TRUE).
show.plot.title: Logical scalar, whether to show the plot title or not (default is set to TRUE).
plot.title: The plot title in the string format (default is set to "Centrality Measure-based Network").
title.position: The position of title ("left", "center", or "right"). The default is set to "center".
show.bottom.border: Logical scalar, whether to draw the bottom border line (default is set to TRUE).
show.left.border: Logical scalar, whether to draw the left border line (default is set to TRUE).
seed: A single value, interpreted as an integer to be used for random number generation for preparing the network layout (default is set to 1234).

Value

A plot with the class ggplot.

Examples

if (FALSE) { # \dontrun{
MyData <- coexpression.data
My_graph <- graph_from_data_frame(MyData)
Graph_IVI <- ivi(graph = My_graph, mode = "all")
Graph_IVI_plot <- cent_network.vis(graph = My_graph, cent.metric = Graph_IVI,
                                   legend.title = "IVI",
                                   plot.title = "IVI-based Network")
} # }

Usage

Arguments

Value

See also

Examples