miic (version 2.0.3)

export: Export miic result for plotting (with igraph)

Description

This function creates an object built from the result returned by miic that is ready to be fed to the plotting method.

Usage

export(
  miic_obj,
  method = "igraph",
  pcor_palette = NULL,
  display = "compact",
  show_self_loops = TRUE
)

Value

A graph object adapted to the method.

Arguments

miic_obj

[a miic object, required]

The object returned by the miic execution.

method

[a string, optional, default value "igraph"]

The plotting method, currently only "igraph" is supported.

pcor_palette

[a color palette, optional, default value grDevices::colorRampPalette(c("blue", "darkgrey", "red")]

Used to represent the partial correlations (the color of the edges). The palette must be able to handle 201 shades to cover the correlation range from -100 to +100.

display

[a string, optional, default value "compact"]

Used only when exporting object returned by miic in temporal mode. It allows different representations of the temporal graph. Possible values are "raw", "lagged", "compact", "combine", "unique", "drop":

• When display = "raw", the export function will use the tmiic graph object as it, leading to the return of a lagged graph.

• When display = "lagged", the export function will repeat the edges over history assuming stationarity and return a lagged graph.

• When display = "compact", the default, nodes and edges are converted into a flattened version to produce a compact view of the temporal network whilst still presenting all the information in the export.
  e.g. X_lag1->Y_lag0, X_lag2<-Y_lag0 become respectively X->Y lag=1, X<-Y lag=2.

• When display = "combine", prior to the export, a pre-processing will be applied to kept only one edge per pair of nodes. The info_shifted will be the highest one of the summarized edges whilst the lag and orientation of the summarized edge will be an aggregation.
  e.g. X_lag2->Y_lag0, X_lag0<-Y_lag1 will become X<->Y lag=1-2 with the info_shifted of X_lag2->Y_lag0 if info_shifted of X_lag2->Y_lag0 > X_lag0<-Y_lag1.

• When display = "unique", prior to the export, a pre-processing will be applied to kept only the edges having the highest info_shifted for a pair of nodes. If several edges between the sames nodes have the same info_shifted, then the edge kept is the one with the minimum lag.
  e.g. X_lag1->Y_lag0, X_lag0<-Y_lag2 with info_shifted of X_lag1->Y_lag0 > X_lag0<-Y_lag2 become X->Y lag=1.

• When display = "drop", the same pre-processing as "unique" will be applied, then the lag information will be dropped before the export.

show_self_loops

[a boolean, optional, TRUE by default]

Used only when exporting object returned by miic in temporal mode. When TRUE, the lagged edges starting and ending on the same node are included in the igraph object. When FALSE, only edges having different nodes are present in the igraph object.

Details

The behavior depends on the method used for the export.

For igraph, edge attributes are passed to the igraph graph and can be accessed with e.g. E(g)$partial_correlation. See miic for more details on edge parameters. By default, edges are colored according to the partial correlation between two nodes conditioned on the conditioning set (negative is blue, null is gray and positive is red) and their width is based on the conditional mutual information minus the complexity cost.

Examples

# \donttest{
library(miic)
data(hematoData)

# execute MIIC (reconstruct graph)
miic_obj <- miic(
  input_data = hematoData, latent = "yes",
  n_shuffles = 10, conf_threshold = 0.001
)

# Using igraph
if(require(igraph)) {
g = export(miic_obj, "igraph")
plot(g) # Default visualisation, calls igraph::plot.igraph()

# Specifying layout (see ?igraph::layout_)
l <-layout_with_kk(g)
plot(g, layout=l)

# Override some graphical parameters
plot(g, edge.curved = .2)
plot(g, vertex.shape="none", edge.color="gray85", vertex.label.color="gray10")
}

# In temporal mode, execute MIIC
data(covidCases)
tmiic_obj <- miic(input_data = covidCases, mode = "TS", n_layers = 3, delta_t = 1, mov_avg = 14)

# Plot by default the compact display of the temporal network using igraph
if(require(igraph)) {
g = export (tmiic_obj)
plot(g)

# Plot the raw temporal network using igraph
g = export(tmiic_obj, display="raw")
plot(g)

# Plot the complete temporal network using igraph (completed by stationarity)
g = export(tmiic_obj, display="lagged")
plot(g)

# Specifying layout (see ?igraph::layout_)
l <- layout_on_grid(g, width = 5, height = 3, dim = 2)
plot(g, layout=l)

# For compact temporal display, please be aware that the rendering of
# igraph::plot.igraph() is not optimal when the graph contains
# multiple edges between the same nodes.
# So, the recommend way to plot a compact graph is to use tmiic plotting:
plot(tmiic_obj)
}

# }