Function plot.mhmm plots a directed graph of the parameters of each model
with pie charts of emission probabilities as vertices/nodes.
# S3 method for mhmm
plot(
x,
interactive = TRUE,
ask = FALSE,
which.plots = NULL,
nrow = NA,
ncol = NA,
byrow = FALSE,
row.prop = "auto",
col.prop = "auto",
layout = "horizontal",
pie = TRUE,
vertex.size = 40,
vertex.label = "initial.probs",
vertex.label.dist = "auto",
vertex.label.pos = "bottom",
vertex.label.family = "sans",
loops = FALSE,
edge.curved = TRUE,
edge.label = "auto",
edge.width = "auto",
cex.edge.width = 1,
edge.arrow.size = 1.5,
edge.label.family = "sans",
label.signif = 2,
label.scientific = FALSE,
label.max.length = 6,
trim = 1e-15,
combine.slices = 0.05,
combined.slice.color = "white",
combined.slice.label = "others",
with.legend = "bottom",
ltext = NULL,
legend.prop = 0.5,
cex.legend = 1,
ncol.legend = "auto",
cpal = "auto",
main = "auto",
withlegend,
...
)A hidden Markov model object of class mhmm created with
build_mhmm (or build_mmm or
build_lcm). Multichannel
mhmm objects are automatically transformed into single-channel objects.
See function mc_to_sc for more information on the
transformation.
Whether to plot each cluster in succession or in a grid.
Defaults to TRUE, i.e. clusters are plotted one after another.
If TRUE and which.plots is NULL,
plot.mhmm operates in interactive mode, via menu.
Defaults to FALSE. Ignored if interactive = FALSE.
The number(s) of the requested cluster(s) as an integer
vector. The default NULL produces all plots.
Optional arguments to arrange plots in a grid. Ignored if
interactive = TRUE.
Controls the order of plotting in a grid. Defaults to FALSE,
i.e. plots are arranged column-wise. Ignored if interactive = TRUE.
Sets the proportions of the row heights of the grid. The default
value is "auto" for even row heights. Takes a vector of values from
0 to 1, with values summing to 1. Ignored if interactive = TRUE.
Sets the proportion of the column heights of the grid. The default
value is "auto" for even column widths. Takes a vector of values
from 0 to 1, with values summing to 1. Ignored if interactive = TRUE.
specifies the layout of vertices (nodes). Accepts a
numerical matrix, a layout_ function (without quotation marks),
or either of the predefined options "horizontal" (the
default) and "vertical". Options "horizontal" and
"vertical" position vertices at the same horizontal or vertical
line. A two-column numerical matrix can be used to give x and y coordinates of
the vertices. The layout_ functions available in the
igraph package offer other automatic layouts for graphs.
Are vertices plotted as pie charts of emission probabilities? Defaults to TRUE.
Size of vertices, given as a scalar or numerical vector. The default value is 40.
Labels for vertices. Possible options include
"initial.probs", "names", NA, and a character or
numerical vector. The default "initial.probs" prints the initial
probabilities of the model and "names" prints the names of the
hidden states as labels. NA prints no labels.
Distance of the label of the vertex from its
center. The default value "auto" places the label outside the
vertex.
Positions of vertex labels, relative to
the center of the vertex. A scalar or numerical vector giving
position(s) as radians or one of "bottom" (pi/2 as radians),
"top" (-pi/2), "left" (pi), or
"right" (0).
Font family to be used for
vertex/edge labels. See argument family in par for
more information.
Defines whether transitions back to same states are plotted.
Defines whether to plot curved edges (arcs, arrows)
between vertices. A logical or numerical vector or scalar. Numerical
values specify curvatures of edges. The default value TRUE
gives curvature of 0.5 to all edges. See igraph.plotting for
more information.
Labels for edges. Possible options include
"auto", NA, and a character or numerical vector. The
default "auto" prints transition probabilities as edge labels.
NA prints no labels.
Width(s) for edges. The default "auto" determines
widths according to transition probabilities between hidden states.
Other possibilities are a scalar or a numerical vector of widths.
An expansion factor for edge widths. Defaults to 1.
Size of the arrow in edges (constant). Defaults to 1.5.
Rounds labels of model parameters to specified number of significant digits, 2 by default. Ignored for user-given labels.
Defines if scientific notation should be used to
describe small numbers. Defaults to FALSE, e.g. 0.0001 instead of
1e-04. Ignored for user-given labels.
Maximum number of digits in labels of model parameters. Ignored for user-given labels.
Scalar between 0 and 1 giving the highest probability of transitions that are plotted as edges, defaults to 1e-15.
Scalar between 0 and 1 giving the highest probability of emission probabilities that are combined into one state. The dafault value is 0.05.
Color of the combined slice that includes
the smallest emission probabilities (only if argument
"combine.slices" is greater than 0). The default color is white.
The label for combined states (when argument
"combine.slices" is greater than 0) to appear in the legend.
Defines if and where the legend of state colors is
plotted. Possible values include "bottom" (the default),
"top", "left", and "right". FALSE omits the
legend.
Optional description of (combined) observed states to appear
in the legend. A vector of character strings. See seqplot for
more information.
Proportion used for plotting the legend. A scalar between 0 and 1, defaults to 0.5.
Expansion factor for setting the size of the font for labels in the legend. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase the size.
The number of columns for the legend. The default value
"auto" sets the number of columns automatically.
Optional color palette for (combinations of) observed states.
The default value "auto" uses automatic color palette. Otherwise a
vector of length x$n_symbols is given, i.e. the argument requires a color
specified for all (combinations of) observed states even if they are not
plotted (if the probability is less than combine.slices).
Optional main titles for plots. The default "auto" uses
cluster_names as titles, NULL prints no titles.
Deprecated. Use with.legend instead.
Other parameters passed on to plot.igraph such as
vertex.color, vertex.label.cex, or edge.lty.
Helske S. and Helske J. (2019). Mixture Hidden Markov Models for Sequence Data: The seqHMM Package in R, Journal of Statistical Software, 88(3), 1-32. doi:10.18637/jss.v088.i03
build_mhmm and fit_model for building and
fitting mixture hidden Markov models; plot.igraph for plotting
directed graphs; and mhmm_biofam and mhmm_mvad for
the models used in examples.
# Loading mixture hidden Markov model (mhmm object)
# of the biofam data
data("mhmm_biofam")
# Plotting only the first cluster
plot(mhmm_biofam, which.plots = 1)
if (interactive()) {
# Plotting each cluster (change with Enter)
plot(mhmm_biofam)
# Choosing the cluster (one at a time)
plot(mhmm_biofam, ask = TRUE)
# Loading MHMM of the mvad data
data("mhmm_mvad")
# Plotting models in the same graph (in a grid)
# Note: the plotting window must be high enough!
set.seed(123)
plot(mhmm_mvad,
interactive = FALSE,
# automatic layout, legend on the right-hand side
layout = layout_nicely, with.legend = "right",
# Smaller and less curved edges
edge.curved = 0.2, cex.edge.width = 0.5, edge.arrow.size = 0.7,
vertex.label.pos = -4 * pi / 5, vertex.label.dist = 5
)
}
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