View source: R/plot.stslist.rep.R

plot.stslist.rep | R Documentation |

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.

## 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, seq.alt = NULL, info = TRUE, cex.with.axis = 1, cex.plot, ...)

`x` |
an object of class |

`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 |

`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 |

`dmax` |
maximal theoretical distance, used for the x axis limits. |

`stats` |
if |

`ylab` |
an optional label for the y axis. If set to |

`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 |

`tick.last` |
Logical. Should a tick mark be enforced at the last position on the x-axis? If unspecified, the |

`seq.alt` |
an object of class |

`info` |
Logical. Should coverage info be displayed? Default is |

`cex.with.axis` |
Axis annotation and plotting text and symbols magnification.
See |

`cex.plot` |
Deprecated. Use |

`...` |
further graphical parameters. For more details about the graphical parameter arguments, see |

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"`

.

Alexis Gabadinho and Gilbert Ritschard

## 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)

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