View source: R/ssp-deprecated.R
ssp | R Documentation |
Function ssp
defines the arguments for plotting with
plot.ssp()
or gridplot()
.
ssp(
x,
hidden.paths = NULL,
plots = "obs",
type = "d",
tlim = 0,
sortv = NULL,
sort.channel = 1,
dist.method = "OM",
with.missing = FALSE,
missing.color = NULL,
title = NA,
title.n = TRUE,
cex.title = 1,
title.pos = 1,
with.legend = "auto",
ncol.legend = "auto",
with.missing.legend = "auto",
legend.prop = 0.3,
cex.legend = 1,
hidden.states.colors = "auto",
hidden.states.labels = "auto",
xaxis = TRUE,
xlab = NA,
xtlab = NULL,
xlab.pos = 1,
ylab = "auto",
hidden.states.title = "Hidden states",
yaxis = FALSE,
ylab.pos = "auto",
cex.lab = 1,
cex.axis = 1,
withlegend,
respect_void = TRUE,
...
)
x |
Either a hidden Markov model object of class |
Output from | |
plots |
What to plot. One of |
type |
The type of the plot. Available types are |
tlim |
Indexes of the subjects to be plotted (the default is 0,
i.e. all subjects are plotted). For example, |
sortv |
A sorting variable or a sort method (one of |
sort.channel |
The number of the channel according to which the
|
dist.method |
The metric to be used for computing the distances of the
sequences if multidimensional scaling is used for sorting. One of "OM"
(optimal matching, the default), "LCP" (longest common prefix), "RLCP"
(reversed LCP, i.e. longest common suffix), "LCS" (longest common
subsequence), "HAM" (Hamming distance), and "DHD" (dynamic Hamming distance).
Transition rates are used for defining substitution costs if needed. See
|
with.missing |
Controls whether missing states are included in state
distribution plots ( |
missing.color |
Alternative color for representing missing values
in the sequences. By default, this color is taken from the |
title |
Main title for the graphic. The default is |
title.n |
Controls whether the number of subjects (in the
first channel) is printed in the title of the plot. The default is
|
cex.title |
Expansion factor for setting the size of the font for the title. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase the size. |
title.pos |
Controls the position of the main title of the plot. The default value is 1. Values greater than 1 will place the title higher. |
with.legend |
Defines if and where the legend for the states is plotted.
The default value |
ncol.legend |
(A vector of) the number of columns for the legend(s). The
default |
with.missing.legend |
If set to |
legend.prop |
Sets the proportion of the graphic area used for plotting
the legend when |
cex.legend |
Expansion factor for setting the size of the font for the 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. |
A vector of colors assigned to hidden states. The default
value | |
Labels for the hidden states. The default value
| |
xaxis |
Controls whether an x-axis is plotted below the plot at the
bottom. The default value is |
xlab |
An optional label for the x-axis. If set to |
xtlab |
Optional labels for the x-axis tick labels. If unspecified, the
column names of the |
xlab.pos |
Controls the position of the x-axis label. The default value is 1. Values greater than 1 will place the label further away from the plot. |
ylab |
Labels for the channels shown as labels for y-axes.
A vector of names for each channel
(observations). The default value |
Optional label for the hidden state plot (in the
y-axis). The default is | |
yaxis |
Controls whether or not to plot the y-axis. The default is |
ylab.pos |
Controls the position of the y axis labels (labels for
channels and/or hidden states). Either |
cex.lab |
Expansion factor for setting the size of the font for the axis labels. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase the size. |
cex.axis |
Expansion factor for setting the size of the font for the x-axis tick labels. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase the size. |
withlegend |
Deprecated. Use |
respect_void |
If |
... |
Other arguments to be passed on to |
This function is deprecated, use stacked_sequence_plot()
instead.
Object of class ssp
.
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