Get lineage clone data from the hemibrainr google drive

* Inc. example of co-plotting lineages, FAFB and hemibrain

R/flywire_tracing.R

@@ -606,3 +606,7 @@ flywire_workflow <- function(flywire.id,
 # hidden, caches result for 5min in current session
 sheet_properties.memo <- memoise::memoise(googlesheets4::sheet_properties, ~memoise::timeout(5*60))
 
+
+library(fafbseg)
+id = fafb14_to_flywire_ids("10655926",only.biggest = TRUE)
+flywire_ntplot(id$flywire.id, cleft.threshold = 30, local = local)

R/lineage_clones.R

@@ -0,0 +1,125 @@
+
+
+#' Download light-level lineage clone data from Ito et al. 2013 or Yu et al. 2013
+#'
+#'@description Get registered light-level clonal data of central brain, secondary developmental lineages. Most neurons in the fly brain hail from one of these lineages.
+#'You can find their meta information in \code{\link{hemibrain_hemilineages}}.
+#'
+#' @param x a specific lineage, e.g. ALlv1. If \code{NULL}, the default, all lineages are fetched
+#' @param brain the brainspace in which hemibrain neurons have been registered. Defaults to raw voxel space for the FlyWire project.
+#' @param dataset whether to get clonal data from Ito et al. 2013 \code{"Ito"} or Yu et al. 2013 \code{"Lee"}.
+#' @param local \code{FALSE} or path. By default (\code{FALSE}) data is read from \code{options()$Drive_hemibrain_data}), but the user can specify an alternative path.
+#'
+#' @references Ito M, Masuda N, Shinomiya K, Endo K, Ito K.
+#' Systematic analysis of neural projections reveals clonal composition of the Drosophila brain.
+#' Curr Biol. 2013 Apr 22;23(8):644-55. doi: 10.1016/j.cub.2013.03.015. Epub 2013 Mar 28. PMID: 23541729.
+#'
+#' @references Yu HH, Awasaki T, Schroeder MD, Long F, Yang JS, He Y, Ding P, Kao JC, Wu GY, Peng H, Myers G, Lee T.
+#' Clonal development and organization of the adult Drosophila central brain. Curr Biol. 2013 Apr 22;23(8):633-43.
+#' doi: 10.1016/j.cub.2013.02.057. Epub 2013 Mar 28. PMID: 23541733; PMCID: PMC3637848.
+#'
+#' @examples
+#' \donttest{
+#' \dontrun{
+#' # Loads all processed flywire neurons as a neuronlistfh object
+#' lee.lins = lineage_clones(brain = "FAFB14", dataset = "Lee")
+#' ito.lins = lineage_clones(brain = "FAFB14", dataset = "Ito")
+#'
+#' # Plot WEDd1
+#' lee.lins.wedd1 = subset(lee.lins, ItoLee_Lineage == "WEDd1")
+#' nopen3d()
+#' plot3d(xyzmatrix(lee.lins.wedd1),
+#' add = TRUE, col = hemibrain_bright_colors["blue"])
+#'
+#' # Plot WEDd1 from the other clonal data set
+#' ito.lins.wedd1 = subset(ito.lins, ItoLee_Lineage == "WEDd1")
+#' nopen3d()
+#' plot3d(xyzmatrix(ito.lins.wedd1),
+#' add = TRUE, col = hemibrain_bright_colors["cyan"])
+#'
+#' # Get flywire neurons
+#' fw.neurons = flywire_neurons()
+#' fw.neurons.wedd1 = subset(fw.neurons, ItoLee_Hemilineage == "WEDd1")
+#' plot3d(fw.neurons.wedd1,
+#' col = hemibrain_bright_colors["red"], soma = 4000)
+#'
+#' # What are the equivalent hemibrain neurons?
+#' cbf.hl = subset(hemibrain_hemilineages, ItoLee_Lineage == "WEDd1")
+#' hb.neurons = hemibrain_neurons(brain="FAFB14")
+#' hb.neurons.wedd1 = subset(hb.neurons,cellBodyFiber%in%cbf.hl$cellBodyFiber)
+#' plot3d(hb.neurons.wedd1, col = hemibrain_bright_colors["orange"], soma = 4000)
+#'
+#'}}
+#'@return A \code{neuronlist} object containing flywire skeletons. In the meta-data, it might be useful for some users to note that
+#'you will get:
+#'
+##' \itemize{
+##'  \item{"flywire.id"}{ The ID given to the corresponding volumetric body in flywire.
+##'  These are used to do things like fetch volumes and are the input to the \code{skeletor} function. However, they are highly volatile and
+##'  change a lot with active tracing.}
+##'  \item{"flywire.xyz"}{ The voxel coordinate of a single point in this neuron, usually a cell body fiber tract position. This is a more accurate way
+##'  of keeping tract of neuron as it will always correspond to the same 'neuron' even though its related flywire.id will change with merge/split events in flywire.}
+##'  \item{"hemilineage"}{ An estimated hemilineage identity from both of two naming systems, Ito et al. 2013 and Wong et al. 2013}
+##'  \item{"side"}{ An estimate as to the 'side', i.e. brain hemisphere, in which the neuron lies}
+##'  \item{"skid"}{ The 'skeleton ID' of this neuron's match in CATMAID for FAFBv14}
+##'  \item{"FAFB.xyz"}{ The coordinates in nanometres of a point in the neuron, in FAFBv14 space}
+##'  \item{"hemibrain_match"}{ The bodyid of an estimated hemibrain match}
+##' }
+#'
+#'@export
+#'@seealso \code{\link{hemibrain_neurons}}, \code{\link{flywire_neurons}}
+lineage_clones <- function(x = NULL,
+                           local = FALSE,
+                           brain = c("FAFB14", "FlyWire", "JRCFIB2018Fraw","JRCFIB2018F","FAFB","JFRC2", "JFRC2013","JRC2018F","FCWB"),
+                           dataset = c("Ito","Lee")
+                           ){
+  brain = match.arg(brain)
+  dataset = match.arg(dataset)
+  if(brain == "JRCFIB2018Fraw"){
+    brain = "JRCFIB2018F"
+    scale = TRUE
+  }else if (brain %in% c("FAFB","FlyWire")){
+    brain = "FAFB14"
+    scale = FALSE
+  }else{
+    scale = FALSE
+  }
+
+  # Get Google drive folder
+  savedir = good_savedir(local = local)
+  neuronsdir = file.path(savedir,"light_level/lineages/")
+  fhdir = file.path(neuronsdir,dataset,brain)
+
+  # Exists?
+  if(!file.exists(fhdir)){
+    stop("Cannot find file: ", fhdir)
+  }
+
+  # Read
+  message("Loading ", fhdir)
+  filelist = list.files(path = fhdir, pattern = ".rds", full.names = TRUE)
+  filelist = sort(filelist,decreasing = TRUE)
+  if(length(filelist)){
+    fh.file = filelist[1]
+    neurons.fh = nat::read.neuronlistfh(fh.file)
+    test = tryCatch(neurons.fh[[1]], error = function(e){
+      warning(e)
+      try(file.remove(paste0(attributes(neurons.fh)$db@datafile,"___LOCK")), silent = FALSE)
+    })
+    attr(neurons.fh,"df") = neurons.fh[,]
+  }else{
+    warning("neuronlistfh (.rds) file not found at: ", fhdir)
+    return(NULL)
+  }
+
+  # Scale neurons if needs be
+  if(scale){
+    neurons.fh = scale_neurons(neurons.fh,scaling=8/1000)
+  }
+
+  # Return
+  if(!is.null(x)){
+    neurons.fh = neurons.fh[names(neurons.fh)%in%x,]
+  }
+  neurons.fh
+}

data-raw/lineage_clones.R

@@ -0,0 +1 @@
+# Make dotprops objects for lineage clones