Plotting the results of species delimitation analyses
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Luke Baton
Feb 10, 2025, 12:09:10 PMFeb 10
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Hi,
Does anyone know if it is possible to easily plot the results of species delimitation analyses using ggtree (or other packages in R)? The type of plot where where multiple "broken" bars/columns, perpendicular to the tree tips, are plotted side-by-side to indicate different species partitions created using different methods. These plots are standard in species delimitation analyses, but in publications no one states how they make their plots, and seems that they do them manually.
It's possible to use the geom_cladelable() function to create such bars, but this requires manual use of the clade node numbers, and manual specification of the bar for each clade within a given partition. This is possible for one or two species partitions, if there are not many divisions within a given partition, but is somewhat tedious, if not impossible, if you have more than a couple of species partitions and/or many divisions within each of them... Furthermore, geom_cladelable() only works with monophyletic groups (which is not always the case for species delimitation analyses). Less importantly, geom_cladelable() also doesn't allow the top (head) of the bar/column to be auotmatically named (for example, a label specifying the method used to create that particular species partition).
What I have in mind is to be able to load a single data.frame specifying all the species partitions in one table (with the specimens represented in the tree tips by row, and the different species partitions in columns), and then be able to plot this data.frame adjacent to the tree (using more-or-less a single command).
A previous discussion on this thread suggested using multiple calls to gheatmap(), but visually this is not a very satisfactory solution, as it creates a column of contiguous cells rather than broken bars, and does not produce quite the kind of plot that is typically made in this kind of research (see: https://groups.google.com/d/msgid/bioc-ggtree/0e7964d8-1a52-4b6b-aed3-386d0b099d4fn%40googlegroups.com).
This seems as if it should be such a simple thing to do, and would be of great value to many researchers!
Any help would be greatly appreciated...
Best wishes to all! Luke
Does anyone know if it is possible to easily plot the results of species delimitation analyses using ggtree (or other packages in R)? The type of plot where where multiple "broken" bars/columns, perpendicular to the tree tips, are plotted side-by-side to indicate different species partitions created using different methods. These plots are standard in species delimitation analyses, but in publications no one states how they make their plots, and seems that they do them manually.
It's possible to use the geom_cladelable() function to create such bars, but this requires manual use of the clade node numbers, and manual specification of the bar for each clade within a given partition. This is possible for one or two species partitions, if there are not many divisions within a given partition, but is somewhat tedious, if not impossible, if you have more than a couple of species partitions and/or many divisions within each of them... Furthermore, geom_cladelable() only works with monophyletic groups (which is not always the case for species delimitation analyses). Less importantly, geom_cladelable() also doesn't allow the top (head) of the bar/column to be auotmatically named (for example, a label specifying the method used to create that particular species partition).
What I have in mind is to be able to load a single data.frame specifying all the species partitions in one table (with the specimens represented in the tree tips by row, and the different species partitions in columns), and then be able to plot this data.frame adjacent to the tree (using more-or-less a single command).
A previous discussion on this thread suggested using multiple calls to gheatmap(), but visually this is not a very satisfactory solution, as it creates a column of contiguous cells rather than broken bars, and does not produce quite the kind of plot that is typically made in this kind of research (see: https://groups.google.com/d/msgid/bioc-ggtree/0e7964d8-1a52-4b6b-aed3-386d0b099d4fn%40googlegroups.com).
This seems as if it should be such a simple thing to do, and would be of great value to many researchers!
Any help would be greatly appreciated...
Best wishes to all! Luke
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