Add Text or Points to Ordination Plots
orditorp.Rd
The function adds 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.
Arguments
- x
A result object from ordination or an
ordiplot
result.- display
Items to be displayed in the plot. Only one alternative is allowed. Typically this is
"sites"
or"species"
.- labels
Optional text used for labels. Row names will be used if this is missing.
- choices
Axes shown.
- priority
Text will be used for items with higher priority if labels overlap. This should be vector of the same length as the number of items plotted.
- select
Items to be displayed. This can either be a logical vector which is
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.- cex, pcex
Text and point sizes, see
plot.default
..- col, pcol
Text and point colours, see
plot.default
.- pch
Plotting character, see
points
.- air
Amount of empty space between text labels. Values <1 allow overlapping text.
- ...
Other arguments to
scores
(and its various methods),text
andpoints
.
Details
Function 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.
Value
The function returns invisibly a logical vector where 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.
Examples
## 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")
# \dontshow{
## example(orditorp) should not set random seed in the user session
rm(.Random.seed)
#> Warning: object '.Random.seed' not found
# }