Visualize EMM objects.
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unused (just for compatibility with the generic for plot in graphics)
see details section.
Project the state centers onto these data. Points which do not belong to any cluster are shown in blue.
a list of parameters for plotting.
further arguments passed on to
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 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
"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):
represent state counts by vertex size?
represent transition counts/probabilities by arrow width?
arrow width. (default: "counts")
Controls the variation of vertex sizes and edge widths (default: 1).
add labels for centers (n/a for
cluster labels to use instead of 1,2,....
Use different markers for points depending on the
state they belong to (only available for MDS when
data is specified).
draw a circle around state centers to indicate the area in which points are assigned to the cluster (experimental, only available for
data is specified).
a vector of state names to be marked and the color(s) used for marking (default: red).
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.,
... is passed on to the
primitive plotting function and can be used to change the plot (colors, etc.)
"graph" the two special parameters "nAttrs" and "eAttrs"
for node and edge attributes can be used.
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data("EMMTraffic") emm <- EMM(threshold=0.2, measure="eJaccard", data=EMMTraffic) op <- par(mfrow = c(2, 2), pty = "s") plot(emm, main="Graph (plain)", parameter=list(cluster_counts=FALSE, arrow_width=FALSE)) plot(emm, main="Graph") plot(emm, method="MDS", main="MDS projection", xlim=c(-0.5,0.5), ylim= c(-0.5,0.5)) plot(emm, method="MDS", data = EMMTraffic, main = "Projection of centers on data") par(op) ## Example to create a fixed layout for igraph g <- as.igraph(emm) l <- layout.star(g) plot(emm, layout=l)
Loading required package: proxy Attaching package: 'proxy' The following objects are masked from 'package:stats': as.dist, dist The following object is masked from 'package:base': as.matrix Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Attaching package: 'rEMM' The following objects are masked from 'package:igraph': as.igraph, clusters
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