read_catmaid_selection: Read a CATMAID selection file

In jefferis/rcatmaid: R access to the API for the CATMAID web image annotation tool

Read a CATMAID selection file

Description

Read a CATMAID selection file

Usage

read_catmaid_selection(f, readNeurons = FALSE, getNames = TRUE, ...)

Arguments

f	Path to the .json file saved by CATMAID
readNeurons	Whether or not to read the neurons listed in the selection file
getNames	Whether to fetch the names of the neurons (default TRUE, ignored if neurons are being fetched)
...	Connection parameters passed to read.neurons.catmaid

Value

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

See Also

write_catmaid_selection

Examples

f=system.file('catmaid-skeletons.json', package = 'catmaid')
read_catmaid_selection(f, getNames=FALSE)
## Not run: 
# read in the neurons for the selection
x=read_catmaid_selection(f, readNeurons=TRUE)
# plot using the CATMAID colour specifications
plot3d(x, col=color)

## End(Not run)

jefferis/rcatmaid documentation built on Aug. 16, 2022, 8:52 p.m.