Not plotting soma after converting to dotprops

natverse / rcatmaid

R package providing API access to the CATMAID web image annotation tool

https://natverse.github.io/rcatmaid

GNU General Public License v3.0

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Not plotting soma after converting to dotprops #88

Open mmc46 opened 6 years ago

mmc46 commented 6 years ago

The soma isn't plotted after converting the neurons to dotprops. Could this be changed?

dl1rsk=catmaid_skids('annotation:glomerulus DL1 right')
dl1rnmirr=fetchn_fafb(dl1rsk, reference = FCWB, mirror = T)
dl1rnmirr.dps=dotprops(x=dl1rnmirr, resample=1, k=5)
open3d()
plot3d(dl1rnmirr, soma=T)
clear3d()
plot3d(dl1rnmirr.dps, soma=T)

jefferis commented 6 years ago

The problem is that the dotprops format has no direct support for plotting cell bodies. It's retrofitted by allowing the metadata data frame attached to a neuronlist to have X,Y,Z columns specifying the soma position.

Presumably you don't want it to plot the soma if there isn't one defined by a soma tag in catmaid?

mmc46 commented 6 years ago

No, not if there isn't one, but these do. I can plot them separately, if there's no easy fix.

jefferis commented 6 years ago

This would require changes in nat and rcatmaid, which I have been pondering for a while since the design isn't really obvious. Part of the implementation is discussed here https://github.com/jefferis/nat/issues/260