text
or points
to
ordination plots. Text will be used if this can be done without
overwriting other text labels, and points will be used otherwise. The
function can help in reducing clutter in ordination graphics, but
manual editing may still be necessary.orditorp(x, display, labels, choices = c(1, 2), priority,
select, cex = 0.7, pcex, col = par("col"), pcol,
pch = par("pch"), air = 1, ...)
ordiplot
result."sites"
or
"species"
.TRUE
for displayed items or a vector of indices
of displayed items. If a logical vector is used, it must have the
same length as the scores plotted.plot.default
..plot.default
.points
.TRUE
means that item was labelled with text and FALSE
means that it
was marked with a point. The returned vector can be used as the
select
argument in ordination text
and points
functions.orditorp
will add either text or points to an existing
plot. The items with high priority
will be added first
and text
will be used if this can be done without
overwriting previous labels,and points
will be used
otherwise. If priority
is missing, labels will be added from the
outskirts to the centre. Function orditorp
can be used
with most ordination results, or plotting results from
ordiplot
or ordination plot functions
(plot.cca
, plot.decorana
,
plot.metaMDS
). Arguments can be passed to the relevant scores
method
for the ordination object (x
) being drawn. See the relevant
scores
help page for arguments that can be used.
## A cluttered ordination plot :
data(BCI)
mod <- cca(BCI)
plot(mod, dis="sp", type="t")
# Now with orditorp and abbreviated species names
cnam <- make.cepnames(names(BCI))
plot(mod, dis="sp", type="n")
stems <- colSums(BCI)
orditorp(mod, "sp", label = cnam, priority=stems, pch="+", pcol="grey")
## show select in action
set.seed(1)
take <- sample(ncol(BCI), 50)
plot(mod, dis="sp", type="n")
stems <- colSums(BCI)
orditorp(mod, "sp", label = cnam, priority=stems, select = take,
pch="+", pcol="grey")
## example(orditorp) should not set random seed in the user session
rm(.Random.seed)
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