mrn_plot | R Documentation |
This function will plot a Multiplex Recurrence Network from a list of igraph objects that can be considered the layers of a network. or based on the output of function mrn()
. The layers must have the same number of nodes.
mrn_plot(
layers = NA,
MRN = NA,
MRNweightedBy = c("InterLayerMI", "EdgeOverlap")[1],
win = NA,
step = NA,
overlap = NA,
alignment = "r",
cumulative = FALSE,
doPlot = TRUE,
doSave = FALSE,
coords = NA,
RNnodes = FALSE,
vertexSizeBy = "degree",
scaleVertexSize = c(0.01, 5),
vertexColour = NA,
vertexBorderColour = "black",
showVertexLegend = TRUE,
showSizeLegend = FALSE,
alphaV = 0.7,
scaleEdgeSize = 1/5,
alphaE = 0.5,
showEdgeColourLegend = FALSE,
curvature = -0.2,
title = "",
createAnimation = FALSE,
useImageMagick = FALSE,
loopAnimation = TRUE,
transitionLength = 3,
stateLength = 1,
gifWidth = 600,
gifRes = 150,
noParts = TRUE,
imageDir = NA,
silent = TRUE
)
layers |
A list of igraph objects representing the layers of the multiplex network. The layer networks must all have the same number of vertices. |
MRN |
The output from function |
MRNweightedBy |
The measure to be used to evaluate the average structural similarities between the layers of the network. Valid options are: |
win |
The window size passed to |
step |
The stepsize for the sliding window (default = |
overlap |
The window overlap passed to |
alignment |
Whether to right ( |
cumulative |
To make the network represent cumulative time, set |
doPlot |
Plot the multiplex recurrence network (default = |
doSave |
Save the plots. |
coords |
A data frame with layout coordinates generated by calling any of the igraph layout functions. If |
RNnodes |
Should the vertices of the MRN represent a plot of the RN of the layers? This is recommended only for a small numbers of vertices. (default = 'FALSE“) |
vertexSizeBy |
A valid igraph function that calculates node based measures, or a numeric constant. (default = |
scaleVertexSize |
Scale the size of the vertices by setting a range for |
vertexColour |
A vector of colours for the vertices. If this is a named list, names will be displayed in the legend. |
vertexBorderColour |
Draw a border around the vertices. Pass |
showVertexLegend |
Show the vertex colour legend? |
showSizeLegend |
Should a legend be shown for the size of the nodes? (default = |
alphaV |
Set transparency for Vertices (default = |
scaleEdgeSize |
Scale the size of the edges by a constant: |
alphaE |
Set transparency for Edges. A single numeric, or a vector of length |
showEdgeColourLegend |
Should a legend be shown for the colour of the edges? (default = |
curvature |
The |
title |
A title for the plot |
createAnimation |
If |
useImageMagick |
Should ImageMagick be used to create the animation. NOTE: ImageMagick has to be installed on your system, see |
loopAnimation |
Should the animation loop? (default = |
transitionLength |
Length of each transition in the animation, ignored if |
stateLength |
Value of |
gifWidth |
Width of the animated |
gifRes |
Resolution of the animated |
noParts |
Do not plot the individual graphs that make up the animation to the current |
imageDir |
Directory to save the layer images and windowed MRN plots. If |
silent |
Silent-ish mode |
A matrix with edge weights between layers that represent the measure MRNweightedBy
.
#' # Create some layers
library(igraph)
layers <- list(g1 = igraph::sample_smallworld(1, 100, 5, 0.05),
g2 = igraph::sample_smallworld(1, 100, 5, 0.5),
g3 = igraph::sample_smallworld(1, 100, 5, 1))
mrn_plot(layers = layers,showEdgeColourLegend=TRUE)
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