help sqindexplot(SJ6-4: st0111)

Title

sqindexplot -- Sequence index plots

Syntax

sqindexplot
[if] [in]
[, options]

ranks(numlist) restrict tabulation on most frequent
numlist

se apply same elements similarity

so apply same order similarity

order(varlist) specify order of vertical axis

by(varname) plot groups of sequences based on varname

color(colorstyle) apply colors to the elements

overplot(#) fine tune bar-width

rbar bars intead of spikes

gapinclude include sequences with gaps in the tabulation

subsequence(a,b) use only subsequence between positions a and b

twoway_options options allowed with graph twoway

Description

sqindexplot draws sequence index plots. These plots draw a
horizontal line for each sequence, which changes its colors according
to the elements.

Out of the box, sequence index plots have several shortcomings, which
should be dealt with when fine-tuning the graph:

o In general, colored versions of sequence index plots are
more sensible than black-and-white versions. The color() opton allows
fine-tuning of the colors used for the elements.

o Depending on variables such as the resulution of the screen,
the viewer used to show the figure, the resolution of the printer, or
the graph size, there can be a tendency to either overplot the lines,
which overrepresents elements with higher category values (levels) or
to have white stripes between the lines. The effect can be moderated
by tuning the option overplot() and/or the
aspectratio. It might also be sensible to restrict the graph to the
most frequent sequences by using the ranks() option.

o Sequence index plots depend heavily on the order of
the sequences along the vertical axis. Without further options, a naive
algorithm is used to order the sequences; however, the order() option
sorts the sequences according to a user-defined variable list. It is
sensible to use the results of sqom to order the sequences in a
sequence index plot.

Options

ranks(numlist) is used to restrict the output to the
most frequent sequences. numlist refers to the position of the
sequences in the sorted frequency table. Hence, ranks(1) refers to the
most frequent sequence, whereas ranks(1/10) refers to the 10 most frequent
sequences. You can also specify ranks(2(2)20).

se is used to request that a plot showing only the elements of
sequences are used (same elements similarity). Hence, with this
option sequences like A-B-A-B, B-A-A-B, and A-B-B-A would be
drawn as A-B.

so is used to request a plot where only the order of
elements is shown (same-order similarity). With this option the
sequences A-B-B-A and A-B-A-A would both be drawn as if they were
A-B-A.

order(varlist) is used to control the order of
the sequences along the vertical axis. Without this option, a simple
algorithm for the order is used. However, an order derived from an
application of sqom is preferable. Note that within sequences
with the same pattern on the order variables the default algorithm is
applied.

by(varname) specifies to plot groups of sequences separately
based on varname.

color(colorstyle) specifies the colors for the
elements. You can specify one color for each element, whereby the
first color refers to the element with the lowest level. See
colorstyle for a list of color choices.

overplot(#) lets you fine-tune the amount of
overplotting. The command tries to be smart about this setting, but
the solutions are not always satisfying, especially with either rather
small or rather large numbers of sequences. The default setting is
overplot(60). Choose a smaller number if the lines for higher
levels appear to thicker than lines for lower levels. Choose a larger
number if there are white stripes between the lines. If you have only
few observations and/or draw sequence index plots with option by(),
you may want to use option rbar.

rbar uses bars instead of spike to draw the
sequences. This option leads to serious overplotting even for moderate
number of observations but can be advantageous for small sample sizes
of when plots are drawn with option by(). rbar.

gapinclude is used to include sequences with gaps. The
default behavior is to drop sequences with gaps from the graph.
The term gap refers only to missing values on the element
variable within a sequence. Sequences with missing values at the
begining and at the end of a sequence are included in any case. You
might consider using sqset with option trim to get rid of
superfluous missings (see sq for details.)

subsequence(a,b) is used to include only the part of
the sequence that is between position a and b, whereby a and b refer
to the position defined in order variable.

twoway_options are a set of common options supported by all
twoway commands; see twoway_options.

Examples

. sqindexplot

. sqindexplot, color(black red yellow)

. sqindexplot, so

. sqindexplot, se

Author

Ulrich Kohler, University of Potsdam, ulrich.kohler@uni-potsdam.de

Also see

Manual: [G] graph, [G] graph twoway rbar, [G] barlook options

Online: sq, sqdemo, sqset,
sqdes, sqegen, sqstat, sqindexplot, sqmodalplot
sqparcoord, sqom, sqclusterdat,
sqclustermat