plot.hmm {seqHMM}

Plot hidden Markov models

Description

Function plot.hmm plots a directed graph with pie charts of emission probabilities as vertices/nodes.

Usage

## S3 method for class 'hmm'
plot(
  x,
  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",
  cpal.legend = "auto",
  legend.order = TRUE,
  main = NULL,
  withlegend,
  ...
)

Arguments

x

A hidden Markov model object of class hmm created with build_hmm (or build_mm). Multichannel hmm objects are automatically transformed into single-channel objects. See function mc_to_sc for more information on the transformation.

layout

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.

pie

Are vertices plotted as pie charts of emission probabilities? Defaults to TRUE.

vertex.size

Size of vertices, given as a scalar or numerical vector. The default value is 40.

vertex.label

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.

vertex.label.dist

Distance of the label of the vertex from its center. The default value "auto" places the label outside the vertex.

vertex.label.pos

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).

vertex.label.family, edge.label.family

Font family to be used for vertex/edge labels. See argument family in par for more information.

loops

Defines whether transitions back to same states are plotted.

edge.curved

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.

edge.label

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.

edge.width

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.

cex.edge.width

An expansion factor for edge widths. Defaults to 1.

edge.arrow.size

Size of the arrow in edges (constant). Defaults to 1.5.

label.signif

Rounds labels of model parameters to specified number of significant digits, 2 by default. Ignored for user-given labels.

label.scientific

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.

label.max.length

Maximum number of digits in labels of model parameters. Ignored for user-given labels.

trim

Scalar between 0 and 1 giving the highest probability of transitions that are plotted as edges, defaults to 1e-15.

combine.slices

Scalar between 0 and 1 giving the highest probability of emission probabilities that are combined into one state. The dafault value is 0.05.

combined.slice.color

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.

combined.slice.label

The label for combined states (when argument "combine.slices" is greater than 0) to appear in the legend.

with.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.

ltext

Optional description of (combined) observed states to appear in the legend. A vector of character strings. See seqplot for more information.

legend.prop

Proportion used for plotting the legend. A scalar between 0 and 1, defaults to 0.5.

cex.legend

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.

ncol.legend

The number of columns for the legend. The default value "auto" sets the number of columns automatically.

cpal

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).

cpal.legend

Optional color palette for the legend, only considered when legend.order is FALSE. Should match ltext.

legend.order

Whether to use the default order in the legend, i.e., order by appearance (first by hidden state, then by emission probability). TRUE by default.

main

Main title for the plot. Omitted by default.

withlegend

Deprecated. Use with.legend instead.

...

Other parameters passed on to plot.igraph such as vertex.color, vertex.label.cex, or edge.lty.

See Also

build_hmm and fit_model for building and fitting Hidden Markov models, mc_to_sc for transforming multistate hmm objects into single-channel objects, hmm_biofam and hmm_mvad for information on the models used in the examples, and plot.igraph for the general plotting function of directed graphs.

Examples

# Multichannel data, left-to-right model

# Loading a HMM of the biofam data
data("hmm_biofam")

# Plotting hmm object
plot(hmm_biofam)

# Plotting HMM with
plot(hmm_biofam,
  # varying curvature of edges
  edge.curved = c(0, -0.7, 0.6, 0.7, 0, -0.7, 0),
  # legend with two columns and less space
  ncol.legend = 2, legend.prop = 0.4,
  # new label for combined slice
  combined.slice.label = "States with probability < 0.05"
)

# Plotting HMM with given coordinates
plot(hmm_biofam,
  # layout given in 2x5 matrix
  # x coordinates in the first column
  # y coordinates in the second column
  layout = matrix(c(
    1, 3, 3, 5, 3,
    0, 0, 1, 0, -1
  ), ncol = 2),
  # larger vertices
  vertex.size = 50,
  # straight edges
  edge.curved = FALSE,
  # thinner edges and arrows
  cex.edge.width = 0.5, edge.arrow.size = 1,
  # varying positions for vertex labels (initial probabilities)
  vertex.label.pos = c(pi, pi / 2, -pi / 2, 0, pi / 2),
  # different legend properties
  with.legend = "top", legend.prop = 0.3, cex.legend = 1.1,
  # Fix axes to the right scale
  xlim = c(0.5, 5.5), ylim = c(-1.5, 1.5), rescale = FALSE,
  # all states (not combining states with small probabilities)
  combine.slices = 0,
  # legend with two columns
  ncol.legend = 2
)

# Plotting HMM with own color palette
plot(hmm_biofam,
  cpal = 1:10,
  # States with emission probability less than 0.2 removed
  combine.slices = 0.2,
  # legend with two columns
  ncol.legend = 2
)

# Plotting HMM without pie graph and with a layout function
require("igraph")
# Setting the seed for a random layout
set.seed(1234)
plot(hmm_biofam,
  # Without pie graph
  pie = FALSE,
  # Using an automatic layout function from igraph
  layout = layout_nicely,
  vertex.size = 30,
  # Straight edges and probabilities of moving to the same state
  edge.curved = FALSE, loops = TRUE,
  # Labels with three significant digits
  label.signif = 3,
  # Fixed edge width
  edge.width = 1,
  # Remove edges with probability less than 0.01
  trim = 0.01,
  # Hidden state names as vertex labels
  vertex.label = "names",
  # Labels insidde vertices
  vertex.label.dist = 0,
  # Fix x-axis (more space on the right-hand side)
  xlim = c(-1, 1.3)
)


# Single-channel data, unrestricted model

# Loading a hidden Markov model of the mvad data (hmm object)
data("hmm_mvad")

# Plotting the HMM
plot(hmm_mvad)

# Checking the order of observed states (needed for the next call)
require(TraMineR)
alphabet(hmm_mvad$observations)

# Plotting the HMM with own legend (note: observation "none" nonexistent in the observations)
plot(hmm_mvad,
  # Override the default order in the legend
  legend.order = FALSE,
  # Colours in the pies (ordered by the alphabet of observations)
  cpal = c("purple", "pink", "brown", "lightblue", "orange", "green"),
  # Colours in the legend (matching to ltext)
  cpal.legend = c("orange", "pink", "brown", "green", "lightblue", "purple", "gray"),
  # Labels in the legend (matching to cpal.legend)
  ltext = c("school", "further educ", "higher educ", "training", "jobless", "employed", "none")
)

require("igraph")
plot(hmm_mvad,
  # Layout in circle (layout function from igraph)
  layout = layout_in_circle,
  # Less curved edges with smaller arrows, no labels
  edge.curved = 0.2, edge.arrow.size = 0.9, edge.label = NA,
  # Positioning vertex labels (initial probabilities)
  vertex.label.pos = c("right", "right", "left", "left", "right"),
  # Less space for the legend
  legend.prop = 0.3
)