Plot method for state sequence objects

Share:

Description

This is the plot method for state sequence objects of class stslist created by the seqdef function. It produces a sequence index plot.

Usage

1
2
3
4
5
## S3 method for class 'stslist'
plot(x, tlim=NULL, weighted=TRUE, sortv=NULL,
    cpal=NULL, missing.color=NULL,
    ylab, yaxis = TRUE, xaxis = TRUE, ytlab = NULL, ylas=0,
    xtlab = NULL, xtstep = NULL, cex.plot=1, ...)

Arguments

x

A state sequence object created with the seqdef function.

tlim

Indexes of the sequences to be plotted (default value is 1:10), for instance 20:50 to plot sequences 20 to 50, c(2,8,12,25) to plot sequences 2,8,12 and 25 in seqdata. If set to 0, all sequences in seqdata are plotted.

weighted

Logical: Should the bar representing each sequence be proportional to its weight? Ignored when no weights are assigned to sequences (see seqdef.)

sortv

A sorting variable or a sort method (one of "from.start" or "from.end"). See details.

cpal

alternative color palette to use for the states. If user specified, a vector of colors with number of elements equal to the number of states in the alphabet. By default, the cpal attribute of the seqdata sequence object is used (see seqdef).

missing.color

alternative color for representing missing values inside the sequences. By default, this color is taken from the "missing.color" attribute of the x sequence object.

ylab

An optional label for the y axis. If set to NA, no label is drawn.

yaxis

Controls whether the y axis is plotted or not. When set to TRUE, sequence indexes are displayed.

xaxis

if TRUE (default), the x (time) axis is plotted.

ytlab

the labels of the plotted sequences to display on the y axis. Default is the indexes of the sequences as defined by the tlim argument. Can be set to "id" for displaying the row names (id) of the sequences instead of their indexes; row names can be assigned to the sequence object with the id argument of the seqdef function or afterwards with rownames. Otherwise ytlab can be set to a vector of length equal to the number of sequences to be plotted.

ylas

sets the orientation of the sequence labels appearing on the y axis. Accepted values are the same as for the las standard option
0: always parallel to the axis (default),
1: always horizontal,
2: always perpendicular to the axis,
3: always vertical.

xtlab

optional labels for the x axis ticks labels. If unspecified, the column names of the seqdata sequence object are used (see seqdef).

xtstep

optional interval at which the tick-marks and labels of the x-axis are displayed. For example, with xtstep=3 a tick-mark is drawn at position 1, 4, 7, etc... The display of the corresponding labels depends on the available space and is dealt with automatically. If unspecified, the xtstep attribute of the x object is used.

cex.plot

expansion factor for setting the size of the font for the axis labels and names of the axes. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase it.

...

arguments to be passed to the plot function or other graphical parameters.

Details

This is the default plot method for state sequence objects (produced by the seqdef function), i.e., for objects of class stslist. It produces a sequence index plot, where individual sequences are rendered with stacked bars depicting the states over time.

This method is called by the generic seqplot function (if type="i"). The latter produces more sophisticated plots, allowing grouping and automatic display of the state color legend. The seqiplot function is a shortcut for calling seqplot with type="i".

When a sortv variable is provided to seqiplot or seqIplot, its values define the order in which the sequences are plotted. With sortv = "from.start", sequence are sorted by the elements of the alphabet at the successive positions starting from the beginning of the sequences. The "from.end" method proceeds similarly, but backward from the last position.

The interest of sequence index plots has for instance been stressed by Scherer (2001) and Brzinsky-Fay et al. (2006). Notice that such index plots for thousands of sequences result in very heavy graphic files if they are stored in PDF or POSTSCRIPT format. To reduce the size, we suggest saving the figures in bitmap format by using for instance png instead of postscript or pdf.

See Also

seqplot

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
## Defining a sequence object with the data in columns 10 to 25
## (family status from age 15 to 30) in the biofam data set
data(biofam)
biofam.lab <- c("Parent", "Left", "Married", "Left+Marr",
"Child", "Left+Child", "Left+Marr+Child", "Divorced")
biofam.seq <- seqdef(biofam, 10:25, labels=biofam.lab)

## Plot of the 10 most frequent sequences
## with bar width proportional to the frequency
plot(biofam.seq)

## Plotting the all data set
## with no borders
plot(biofam.seq, tlim=0, space=0, border=NA)

## =======
## Weights
## =======
data(ex1)
ex1.seq <- seqdef(ex1, 1:13, weights=ex1$weights)
plot(ex1.seq)
plot(ex1.seq, weighted=FALSE)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.