Subset neuronlist returning either new neuronlist or names of chosen neurons

# S3 method for neuronlist
  rval = c("neuronlist", "names", "data.frame"),



a neuronlist


An expression that can be evaluated in the context of the dataframe attached to the neuronlist. See details.


a function which can be applied to each neuron returning TRUE when that neuron should be included in the return list.


What to return (character vector, default='neuronlist')


additional arguments passed to filterfun


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


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).

See also


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)
#> gene_name Name idid soma_side #> GadMARCM-F000142_seg002 GadMARCM-F000142_seg002 Gad1-F-300043 10647 L #> GadMARCM-F000423_seg001 GadMARCM-F000423_seg001 Gad1-F-300107 9541 R #> ChaMARCM-F000586_seg002 ChaMARCM-F000586_seg002 Cha-F-300150 7113 R #> flipped Driver Gender X Y Z #> GadMARCM-F000142_seg002 FALSE Gad1-Gal4 F 349.5917 78.18986 96.69280 #> GadMARCM-F000423_seg001 TRUE Gad1-Gal4 F 401.4795 76.32671 97.92564 #> ChaMARCM-F000586_seg002 TRUE Cha-Gal4 F 340.1020 79.79322 92.21622 #> exemplar cluster idx type #> GadMARCM-F000142_seg002 GadMARCM-F000142_seg002 71 1535 apbp #> GadMARCM-F000423_seg001 GadMARCM-F000423_seg001 61 1265 apbp #> ChaMARCM-F000586_seg002 ChaMARCM-F000586_seg002 52 898 apbp
# 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)))) if (FALSE) { # 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') }