plot.cca with optimize=TRUE and ordipointlabel in pipe #674
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Arg 'add = TRUE' needs tweaking: points are currently drawn only with 'add = FALSE'.
10% difference in graphic device dimensions triggers message. mar() is not checked, but it also influences plot size.
- try more times: now 64 (was 48) means that on average each position is tried 8 times (was 6). - a bit more detailed and stronger penalty: now against moving towards origin and against corners.
Triggers false warnings if using args for scores(), for instance.
Function text.ordiplot gains arg 'optimize' to call ordipointlabel to move text to reduce overlap, but put a point in the exact location. Function plot.cca uses text.ordiplot and gains the same ability. For instance, plot(cca(dune), spe.par = list(optimize=TRUE)).
This makes easier to have programmatic use of scores() when input parameter can be a pre-processed matrix instead of a complex list of matrices. Earlier ordipointabel(x, display=what) failed in text.ordiplot() when called from plot.cca().
- global arg (dot argument) 'optimize = T' must be eval'ed to make it logical TRUE (will be symbol initially) - add point defPointPar if pch not given by user - message on arrows looking strange with optimize=TRUE
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This is the second stage of new fully configurable
plot.ccafunctions. This addsoptimize = TRUEargument totext.ordiplotand hence toplot.ccaas @gavinsimpson suggested in #657. With this,ordipointlabelwas made usable inplot/ordiplotpipe. The usage of plotting text over non-transparent label was expanded to more functions with argumentbg = <colour>, usually viaordilabelbut directly implemented inordipointlabel.The real changes were made in base routines used by
plot.cca:ordipointlabelcan be used in anordiplotpipe and can draw text on labels withbg = <colour>. This optimizes any number of score types, although it defaults to two.text.ordiplotgained new argumentoptimize = TRUEthat will callordipointlabelfor one set of scores.plot.ccaonly sanitizes its input and will calltext.ordiplotfor new features.text.ordiplot,ordilabelandordipointlabel(and the two latter are more configurable in pipe than viaplot.cca).I made this as a PR instead of direct merge to allow comments and suggestions before merge, and to make these new capabilities more visible.