Make a CATMAID selection file based on neuronlist or skids

write_catmaid_selection(x, f, color = NULL, opacity = NULL, ...)

Arguments

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 catmaid_skids

See also

Examples

if (FALSE) { # Write selection file for neurons defined by annotation or name write_catmaid_selection("PN", "pns.json") write_catmaid_selection("name:AV6", "name:av6.json") pns=read.neurons.catmaid("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) }