R/soma.R

In natverse/neuprintr: R Client Utilities for Interacting with the neuPrint Connectome Analysis Service

#' @title Get the annotated positions in space for somata
#'
#' @description  For some datasets, somata positions have been mapped to pixels within a soma volume in the image data. If your bodyids contain such an annotated pixel, you can retrieve its position.
#' @inheritParams neuprint_read_neurons
#' @return a data frame of X,Y,Z coordinates, a row for each bodyid supplied
#' @examples
#' \donttest{
#' neuprint_locate_soma("5813115796")
#' }
#' @seealso \code{\link{neuprint_fetch_custom}}, \code{\link{neuprint_get_synapses}}, \code{\link{neuprint_read_neurons}}
#' @export
#' @rdname neuprint_assign_connectors
neuprint_locate_soma <- function(bodyids, dataset = NULL, all_segments = TRUE, conn = NULL, ...){
  all_segments.json = ifelse(all_segments,"Segment","Neuron")
  bodyids = neuprint_ids(bodyids, conn = conn, dataset = dataset, unique=FALSE)
  cypher = sprintf("WITH %s AS bodyIds UNWIND bodyIds AS bodyId MATCH (n:`%s`) WHERE n.bodyId=bodyId RETURN n.bodyId AS bodyId, n.somaLocation AS soma",
                   id2json(bodyids),
                   all_segments.json)
  nc = neuprint_fetch_custom(cypher=cypher, conn = conn, dataset = dataset, ...)
  if(length(nc$data)==0){
    coordinates = matrix(c(NA,NA,NA),nrow=length(bodyids),ncol=3)
    coordinates = cbind(data.frame(bodyid=bodyids),coordinates)
  }else{
    for(i in 1:length(nc$data)){
      if(is.null(nc$data[[i]][[2]]$coordinates)){
        nc$data[[i]][[2]]$coordinates = list(NA,NA,NA)
      }
    }
    coordinates = do.call(rbind,lapply(nc$data,function(x) cbind(x[[1]],rbind(x[[2]]$coordinates))))
    coordinates = as.data.frame(t(apply(coordinates,1,function(r) unlist(r))))
  }
  colnames(coordinates) = c("bodyid","X","Y","Z")
  coordinates
}