New function orditkplot with its support functions for interactive ordination plots. The function will open a new Tcl/Tk window where points are fixed at their ordination scores, but their labels can be moved to better position with mouse or edited. The plot can be exported in various graphics formats or saved in the R session for further manipulation or re-created with R commands.
The function was transferred from vegan where it has been since 2008 (CRAN release 1.11-0).
The function adds a conditional dependency on tcltk package.
ordiplot3d failed if input was a scores matrix instead of being a list-style object.
rgl.isomap could fail mysteriously with some extra arguments (e.g. with type = "p").
ordiplot3d can now set the exact aspect ratio in ordination plots. Earlier we had a kluge that gave approximately correct ratio. The package now depends on scatterplot3d version 0.3-40.ordirgl failed when cex was a variable instead of a number.
orglcluster did not obey display argument but always showed "sites".
orglellipse gained a new option kind = "ehull" to draw ellipsoid hulls or minimum volume ellipsoids that enclose all points of a group. The option is based on ellipsoidhull() function (cluster package).
ordirgl allows suppressing display of environmental variables in constrained ordination with envfit = NA.
orglspider was not exported.orditree3d (based on scatterplot3d) and ordirgltree (based on rgl) draw a cluster dendrogram over a 2D ordination or any other plane, for instance a map.
orglcluster is similar to vegan ordicluster and adds a cluster dendrogam to an ordirgl plot.
orglellipse is similar to vegan ordiellipse and adds standard deviation, standard error or confidence ellipsoids to an ordirgl plot.
orglspantree is similar to vegan lines.spantree and adds a minimum spanning tree to an ordirgl plot.
Users have improved control of colours of plotted items. The colour can be a vector for points or text items plotted, or for groups of items drawn in the graph (orglellipse, orglsegments, orglspider). If the functions draws lines connecting points, the line colour is a mixture of colours of connected points (orditree3d, ordirgltree, orglcluster, orglspantree, rgl.isomap).
ordirgl uses now small spheres instead of points with better visual impact.
ordiplot3d gained a scores function making easier to add 2D items with vegan ordiellipse, ordihull, ordispider, ordisegments etc.