subset.neuronlist: Subset neuronlist returning either new neuronlist or names of...

In nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

Subset neuronlist returning either new neuronlist or names of chosen neurons

Description

Subset neuronlist returning either new neuronlist or names of chosen neurons

Usage

## S3 method for class 'neuronlist'
subset(
  x,
  subset,
  filterfun,
  rval = c("neuronlist", "names", "data.frame"),
  ...
)

Arguments

x	a neuronlist
subset	An expression that can be evaluated in the context of the dataframe attached to the neuronlist. See details.
filterfun	a function which can be applied to each neuron returning TRUE when that neuron should be included in the return list.
rval	What to return (character vector, default='neuronlist')
...	additional arguments passed to filterfun

Details

The subset expression should evaluate to one of

• character vector of names

• logical vector

• vector of numeric indices

Any missing names are dropped with a warning. The filterfun expression is wrapped in a try. Neurons returning an error will be dropped with a warning.

You may also be interested in find.neuron, which enables objects in a neuronlist to be subsetted by a 3D selection box. In addition subset.neuron, subset.dotprops methods exist: these are used to remove points from neurons (rather than to remove neurons from neuronlists).

Value

A neuronlist, character vector of names or the attached data.frame according to the value of rval

See Also

neuronlist, find.neuron, subset.data.frame, subset.neuron, subset.dotprops

Examples

da1pns=subset(Cell07PNs,Glomerulus=='DA1')
with(da1pns,stopifnot(all(Glomerulus=='DA1')))
gammas=subset(kcs20,type=='gamma')
with(gammas,stopifnot(all(type=='gamma')))
# define a function that checks whether a neuron has points in a region in 
# space, specifically the tip of the mushroom body alpha' lobe
aptip<-function(x) {xyz=xyzmatrix(x);any(xyz[,'X']>350 & xyz[,'Y']<40)}
# this should identify the alpha'/beta' kenyon cells only
apbps=subset(kcs20,filterfun=aptip)
# look at which neurons are present in the subsetted neuronlist
head(apbps)
# combine global variables with dataframe columns
odds=rep(c(TRUE,FALSE),10)
stopifnot(all.equal(subset(kcs20,type=='gamma' & odds),
            subset(kcs20,type=='gamma' & rep(c(TRUE,FALSE),10))))
## Not run: 
# make a 3D selection function using interactive rgl::select3d() function
s3d=select3d()
# Apply a 3D search function to the first 100 neurons in the neuronlist dataset
subset(dps[1:100],filterfun=function(x) {sum(s3d(xyzmatrix(x)))>0},
  rval='names')
# combine a search by metadata, neuropil location and 3D location
subset(dps, Gender=="M" & rAL>1000, function(x) sum(s3d(x))>0, rval='name')
# The same but specifying indices directly, which can be considerably faster
# when neuronlist is huge and memory is in short supply
subset(dps, names(dps)[1:100],filterfun=function(x) {sum(s3d(xyzmatrix(x)))>0},
  rval='names')

## End(Not run)

nat documentation built on May 29, 2024, 10:36 a.m.