Make a CATMAID selection file based on neuronlist or skids
write_catmaid_selection(x, f, color = NULL, opacity = NULL, ...)
x | A neuronlist, data.frame or vector of skids |
---|---|
f | Path to output file (usually ends in .json) |
color | Optional vector of colours in any format understood by col2rgb |
opacity | Optional vector of opacities (alpha values) in range 0-1 |
... | Additional arguments passed to |
# NOT RUN { pns=read.neurons.catmaid("annotation:^PN$") # extract the glomerulus from the name pns[, 'glomerulus'] = stringr::str_match(pns[, 'name'], ".*glomerulus ([A-z0-9]+) .*")[, 2] pns[, 'glomerulus']=addNA(factor(pns[, 'glomerulus'])) # get the same colours that nat would normally use in a plot plotres=plot3d(pns, col=glomerulus) cols=attr(plotres,'df')$col # write out selection file with those colours write_catmaid_selection(pns, f='pns-by-glom.json', color=cols) # }