Add colours to the neuroglancer scene

Usage

ngl_add_colours(x, colours, layer = NULL)

Arguments

x: neuroglancer scene in any form acceptable to ngl_decode_scene (including as a URL)
colours: A dataframe with two columns, where the first is the id and the second is the colour, OR a character vector of colours named by the ids or one colour which would be added to all the displayed neurons. See col2rgb for additional details of how col can be specified.
layer: Optional character vector specifying the layer to colour. When lyaer=NULL (the default) will choose a layer of type segmentation_with_graph if one exists.

Value

A neuroglancer scene object (see ngl_decode_scene)

Examples

fw_url=with_segmentation('flywire31', getOption('fafbseg.sampleurl'))
ngl_add_colours(fw_url, colours=c("720575940614404544"="red"))
#> neuroglancer scene with 2 layers and 2 segments (of which 2 shown)
#>                                 name                    type visible nsegs
#> 1                   Production-image                   image    TRUE     0
#> 2 Production-segmentation_with_graph segmentation_with_graph    TRUE     2
#>   nhidden
#> 1       0
#> 2       0
#>                                                                        source
#> 1 precomputed://gs://microns-seunglab/drosophila_v0/alignment/image_rechunked
#> 2          graphene://https://prod.flywire-daf.com/segmentation/table/fly_v31

if (FALSE) {
# colour all neurons in the URL on the clipboard red.
# Then convert back to URL and open in default browser
browseURL(as.character(ngl_add_colours(clipr::read_clip(), col="red")))

# Let's colour neurons from these 3 scenes in red, green and blue
u1="https://ngl.flywire.ai/?json_url=https://globalv1.flywire-daf.com/nglstate/5695474417795072"
u2="https://ngl.flywire.ai/?json_url=https://globalv1.flywire-daf.com/nglstate/5198787572137984"
u3="https://ngl.flywire.ai/?json_url=https://globalv1.flywire-daf.com/nglstate/5673953041317888"
# sequentially build up a data.frame with the colour information
# note that col will be recycled to the same length as the number of segments
colourdf=data.frame(ids=ngl_segments(u1), col='red')
colourdf=rbind(colourdf, data.frame(ids=ngl_segments(u2), col='green'))
colourdf=rbind(colourdf, data.frame(ids=ngl_segments(u3), col='blue'))
# apply that to the first URL
sc=ngl_add_colours(u1, colourdf)
browseURL(as.character(sc))
}