plot.EMM: Visualize EMM Objects

In rEMM: Extensible Markov Model for Modelling Temporal Relationships Between Clusters

Visualize EMM Objects

Description

Visualize EMM objects.

Usage

## S4 method for signature 'EMM,missing'
plot(x, y,
  method=c("igraph", "interactive", "graph", "MDS",
           "cluster_counts", "transition_counts"),
  data = NULL, parameter=NULL, ...)

Arguments

x	an EMM object.
y	unused (just for compatibility with the generic for plot in graphics)
method	see details section.
data	Project the state centers onto these data. Points which do not belong to any cluster are shown in blue.
parameter	a list of parameters for plotting (see Details section).
...	further arguments passed on to plot.default or plot.igraph.

Details

There are several methods for plotting:

"igraph" produces a graph representation of the EMM using igraph. Additional arguments like layout are passed on to plot for igraph.

"interactive" produces an interactive graph representation of the EMM (using igraph). Arguments suitable for plot.igraph in igraph can be passed on as ....

"graph" produces a graph representation of the EMM using Rgraphviz. If Rgraphviz is not installed/available then the method reverts to "igraph".

"MDS" projects the cluster centers into 2-dimensional space.

"cluster_counts" produces a barplot for cluster counts.

"transition_counts" produces a barplot for transition counts.

The following plotting parameters are currently supported (by some of the visualizations):

state_counts

represent state counts by vertex size? (default: TRUE)

arrow_width

represent transition counts/probabilities by arrow width? (default: TRUE)

arrows

use "counts" or "probabilities" for arrow width. (default: "counts")

arrow_width_multiplier, state_size_multiplier

Controls the variation of vertex sizes and edge widths (default: 1).

add_labels

add labels for centers (n/a for type = "graph").

cluster_labels

cluster labels to use instead of 1,2,....

mark_clusters

Use different markers for points depending on the state they belong to (only available for MDS when data is specified).

draw_threshold

draw a circle around state centers to indicate the area in which points are assigned to the cluster (experimental, only available for MDS when data is specified).

mark_states, mark_state_color

a vector of state names to be marked and the color(s) used for marking (default: red).

mark_transitions, mark_transitions_color

a vector of transition names in the format "3->2" to be marked and the color(s) used for marking (default: red).

For some plots (e.g., "igraph") ... is passed on to the primitive plotting function and can be used to change the plot (colors, etc.) See ? igraph.plotting. For "graph" the two special parameters "nAttrs" and "eAttrs" for node and edge attributes can be used.

See Also

EMM

Examples

data("EMMTraffic")

emm <- EMM(threshold = 0.2,
  measure = "eJaccard",
  data = EMMTraffic)

op <- par(mfrow = c(2, 2), pty = "s")

plot(emm, main = "Graph")

## Plot the graph as a tree with a set root node and an aspect ratio of 1:1.
g <- as.igraph(emm)
plot(emm, main = "Graph (tree layout)",
  layout = igraph::layout_as_tree(g, root = 1), asp = 1)

plot( emm, method = "MDS",
  main = "Graph (MDS projection)", xlim = c(-0.5, 0.5), ylim = c(-0.5, 0.5)
)

plot(emm, method = "MDS", data = EMMTraffic,
  main = "Projection of cluster \ncenters on data")
par(op)

rEMM documentation built on May 29, 2024, 4:35 a.m.