Compare a neuroglancer mesh object with a regular neuron

Compare a neuroglancer mesh object with a regular neuron

Usage

compare_ng_neuron(
  x,
  n,
  breaks = 3,
  colpal = c("cyan", "red"),
  plot = TRUE,
  plotn = plot,
  pointsize = 0.1,
  sample_dots = 1,
  ...
)

Arguments

x

A neuroglancer mesh, rgl::mesh3d object or other object with a defined xyzmatrix function.

n

A nat::neuron object

breaks

either a numeric vector of two or more unique cut points or a single number (greater than or equal to 2) giving the number of intervals into which x is to be cut.

colpal

A function defining a colour palette or a vector of colour names. Should

plot

Whether to plot anything (set to FALSE when you just want to get the distance information)

plotn

Whether to plot the neuron n

pointsize

Size of plotted points for mesh - passed on to points3d. Default pointsize=0.1 makes points smaller than usual.

sample_dots

Fraction of points (0-1) from the mesh to plot - the default value of 1 implies all points. Values of sample_dots < 1 select a random subsample of the points.

...

Additional arguments passed to plot3d.neuron

Value

Invisibly, a data.frame with the distances of each object in x

to its nearest neighbour in n as well as the breaks used for colouring points when plotting.

See also

read_brainmaps_meshes to read 3D meshes from remote server, read_segments2 to read skeletons from zip files, and read.neurons and read.neurons.catmaid and friends to read regular neurons from disk or a CATMAID server.

Examples

if (FALSE) {
x=read_ng_raw('meshdata/')
library(elmr)
y=read.neuron.catmaid(23432)
compare_ng_neuron(x,y)
}