R/flycircuit-data.R

In jefferis/flycircuit: Functions to support the analysis of the FlyCircuit single neuron dataset

#' fcidtable - Data.frame of flycircuit identifiers
#' 
#' @details The flycircuit database seems to have at least 3 unique identifiers
#'   for neurons. These are: \itemize{
#'   
#'   \item{idid}{ An integer identifier which ranged from 1:16226 in the April 
#'   2011 release}
#'   
#'   \item{gene_name}{ A character identifier of the general form 
#'   "DvGlutMARCM-F003905_seg001"}
#'   
#'   \item{Name}{ A character identifier of the general form "VGlut-F-400794"}
#'   
#'   }
#'   
#'   Although the neuron \code{Name} is generally what is reported in
#'   publications the \code{gene_name} seems to widely used and is what
#'   connected to the confocal image file name. The \code{_seg001} suffix in
#'   gene_names refers to the segmentation of individual neurons from stacks
#'   that might contain multiple labelled neurons after MARCM.
#'   
#' @name fcidtable
#' @family flycircuit-ids
#' @docType data
NULL

#' FCWB.surf - Surface model of FCWB FlyCircuit reference brain
#' 
#' The FCWB reference brain is a shape averaged template brain generated using 
#' the CMTK avg_adm tool. See
#' \url{https://github.com/jefferislab/MakeAverageBrain} for the relevant code.
#' 
#' @name FCWB.surf
#' @docType data
NULL

#' FCWBNP.surf - Surface model of FlyLight neuropil segmentation in FlyCircuit
#' coordinate space
#' 
#' @name FCWBNP.surf
#' @docType data
NULL

#' A dataframe containing manual annotations of some FlyCircuit neurons
#' 
#' @details \code{neuron_idid} matches \code{idid} of fcidtable
#' @seealso \code{\link{fcidtable}}
#' @name annotation
#' @docType data
NULL

#' A matrix containing all by all nblast similarity scores for 20 neurons
#' 
#' These are the same neurons whose morphology is present in the nat
#' \code{kcs20} neuronlist object.
#' @seealso \code{\link[nat]{kcs20}}
#' @name kcs20scores
#' @docType data
NULL