Read a CATMAID selection file
read_catmaid_selection(f, readNeurons = FALSE, getNames = TRUE, ...)Path to the .json file saved by CATMAID
Whether or not to read the neurons listed in the selection file
Whether to fetch the names of the neurons (default
TRUE, ignored if neurons are being fetched)
Connection parameters passed to read.neurons.catmaid
A data.frame containing the selection information or (if
readNeurons=TRUE) a neuronlist containing this
information in the attached metadata. The columns will be
skid The numeric skeleton id
color The colour of the selected neuron in catmaid
opacity The opacity (alpha value) of the neuron name
name Optionally the name of the neuron
f=system.file('catmaid-skeletons.json', package = 'catmaid')
read_catmaid_selection(f, getNames=FALSE)
#> skid color opacity
#> 1 1180353 #ffff00 1
#> 2 1181286 #ff00ff 1
#> 3 1182615 #0000ff 1
#> 4 1313485 #00ff00 1
#> 5 1334552 #ffffff 1
#> 6 1334561 #00ffff 1
#> 7 1371629 #ff7f00 1
#> 8 2390270 #7fff00 1
#> 9 2390280 #7f7f7f 1
#> 10 3826596 #ff0000 1
#> 11 3842618 #7f7fff 1
#> 12 3853002 #bfbfbf 1
#> 13 3872709 #ff7f7f 1
#> 14 4232956 #7fff7f 1
#> 15 4260599 #ff007f 1
#> 16 1182625 #d8a31e 1
#> 17 1273130 #3fe0d1 1
#> 18 1334538 #ffbfc9 1
#> 19 1338786 #08f62f 1
#> 20 3842350 #f30b61 1
#> 21 3852709 #02fc9f 1
#> 22 3908112 #04fa3f 1
#> 23 3910750 #ffffff 1
#> 24 3927073 #57f608 1
#> 25 3930323 #ff0046 1
#> 26 3931453 #98ff00 1
#> 27 4149101 #89bf3f 1
#> 28 4165941 #00ff51 1
#> 29 4214127 #ff9a00 1
#> 30 4233149 #819cfd 1
#> 31 4260588 #dfae9f 1
#> 32 4276626 #fc82f7 1
#> 33 4311394 #99fa83 1
#> 34 4328317 #1306f8 1
#> 35 4344859 #790a05 1
if (FALSE) {
# read in the neurons for the selection
x=read_catmaid_selection(f, readNeurons=TRUE)
# plot using the CATMAID colour specifications
plot3d(x, col=color)
}