R: Plot method for representative sequence sets

plot.stslist.rep {TraMineR} | R Documentation

## Plot method for representative sequence sets

### Description

This is the plot method for output produced by the `seqrep` function, i.e, for objects of class stslist.rep. It produces a representative sequence plot.

### Usage

    ## S3 method for class 'stslist.rep'
    plot(x, cpal = NULL, missing.color = NULL, pbarw = TRUE,
      dmax = NULL, stats = TRUE, ylab = NULL, xaxis = TRUE, xtlab = NULL,
      xtstep = NULL, tick.last = NULL, cex.with.axis = 1, cex.plot, ...)

### Arguments

`x` | an object of class stslist.rep as produced by the `seqrep` function.
`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 `x` object is used.
`missing.color` | alternative color for representing missing values inside the sequences. By default, this color is taken from the "missing.color" attribute of the sequence object being plotted.
`pbarw` | when `TRUE`, the bar heights are set proportional to the number of represented sequences.
`dmax` | maximal theoretical distance, used for the x axis limits.
`stats` | if `TRUE` (default), mean discrepancy in each subset defined by all sequences attributed to one representative sequence and the mean distance to this representative sequence are displayed.
`ylab` | an optional label for the y axis. If set to `NA`, no label is drawn.
`xaxis` | controls whether a x axis is plotted.
`xtlab` | optional labels for the x axis ticks labels. If unspecified, the column names of the object being plotted.
`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.
`tick.last` | Logical. Should a tick mark be enforced at the last position on the x-axis? If unspecified, the `tick.last` attribute of the `x` object is used.
`cex.with.axis` | Axis annotation and plotting text and symbols magnification. See `par`.
`cex.plot` | Deprecated. Use `cex.with.axis` instead.
`...` | further graphical parameters. For more details about the graphical parameter arguments, see `barplot` and `par`.

### Details

This is the plot method for the output produced by the `seqrep` function, i.e. objects of class stslist.rep. It produces a plot where the representative sequences are displayed as horizontal bars with width proportional to the number of sequences assigned to them. Sequences are plotted bottom-up according to their representativeness score.
Above the plot, two parallel series of symbols associated to each representative are displayed horizontally on a scale ranging from 0 to the maximal theoretical distance D_max. The location of the symbol associated to the representative r_i indicates on axis A the (pseudo) variance (V_i) within the subset of sequences assigned to r_i and on the axis B the mean distance MD_i to the representative.

This method is called by the generic `seqplot` function (if `type="r"`) that produces more sophisticated plots with group splits and automatic display of the color legend. The `seqrplot` function is a shortcut for calling `seqplot` with `type="r"`.

### Author(s)

Alexis Gabadinho (with Gilbert Ritschard for the help page)

### Examples

    ## Loading the mvad data set and creating a sequence object
    data(mvad)
    mvad.labels <- c("employment", "further education", "higher education",
                        "joblessness", "school", "training")
    mvad.scodes <- c("EM","FE","HE","JL","SC","TR")

    ## First 36 months trajectories
    mvad.seq <- seqdef(mvad, 15:50, states=mvad.scodes, labels=mvad.labels)

    ## Computing Hamming distances
    ##
    dist.ham <- seqdist(mvad.seq, method="HAM")

    ## Extracting a representative set using the sequence frequency
    ## as a representativeness criterion
    mvad.rep <- seqrep(mvad.seq, diss=dist.ham)

    ## Plotting the representative set
    plot(mvad.rep)

[Package TraMineR version 2.2-3 Index]