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Update hemibrain_matching.R
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@alexanderbates
alexanderbates committed Jan 6, 2021
1 parent e09ef57 commit eb3617d
Showing 1 changed file with 34 additions and 30 deletions.
64 changes: 34 additions & 30 deletions R/hemibrain_matching.R
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Original file line number Diff line number Diff line change
Expand Up @@ -878,17 +878,19 @@ hemibrain_matches <- function(priority = c("FAFB","hemibrain"),
present = !is.na(hemibrain.matches[[nt]])
missing = is.na(hemibrain.matches$flywire.xyz)
replace = (present+missing)>1
if(nt=="CATMAID.nblast.top"){
hemibrain.matches$FAFB.match[replace] = hemibrain.matches[[nt]][replace]
hemibrain.matches$flywire.xyz[replace] = fafb.matches$flywire.xyz[match(hemibrain.matches$FAFB.match[replace],fafb.matches$skid)]
hemibrain.matches$flywire.id[replace] = fafb.matches$flywire.id[match(hemibrain.matches$FAFB.match[replace],fafb.matches$skid)]
}else{
hemibrain.matches$flywire.id[replace] = hemibrain.matches[[nt]][replace]
hemibrain.matches$flywire.xyz[replace] = fafb.matches$flywire.xyz[match(fafb.matches$flywire.id[replace],fafb.matches$flywire.id)]
hemibrain.matches$FAFB.match[replace] = fafb.matches$skid[match(hemibrain.matches$flywire.id[replace],fafb.matches$flywire.id)]
if(sum(replace)){
if(nt=="CATMAID.nblast.top"){
hemibrain.matches$FAFB.match[replace] = hemibrain.matches[[nt]][replace]
hemibrain.matches$flywire.xyz[replace] = fafb.matches$flywire.xyz[match(hemibrain.matches$FAFB.match[replace],fafb.matches$skid)]
hemibrain.matches$flywire.id[replace] = fafb.matches$flywire.id[match(hemibrain.matches$FAFB.match[replace],fafb.matches$skid)]
}else{
hemibrain.matches$flywire.id[replace] = hemibrain.matches[[nt]][replace]
hemibrain.matches$flywire.xyz[replace] = fafb.matches$flywire.xyz[match(fafb.matches$flywire.id[replace],fafb.matches$flywire.id)]
hemibrain.matches$FAFB.match[replace] = fafb.matches$skid[match(hemibrain.matches$flywire.id[replace],fafb.matches$flywire.id)]
}
hemibrain.matches$FAFB.match.quality[replace] = "NBLAST"
}
}
hemibrain.matches$FAFB.match.quality[replace] = "NBLAST"
}
}

# Set unassigned matches to top.nblast
Expand All @@ -898,8 +900,10 @@ hemibrain_matches <- function(priority = c("FAFB","hemibrain"),
present = !is.na(fafb.matches[[nt]])
missing = is.na(fafb.matches$hemibrain.match)
replace = (present+missing)>1
fafb.matches$hemibrain.match[replace] = fafb.matches[[nt]][replace]
fafb.matches$hemibrain.match.quality[replace] = "NBLAST"
if(sum(replace)){
fafb.matches$hemibrain.match[replace] = fafb.matches[[nt]][replace]
fafb.matches$hemibrain.match.quality[replace] = "NBLAST"
}
}
}

Expand Down Expand Up @@ -1185,7 +1189,6 @@ lm_matches <- function(priority = c("hemibrain","lm"), selected_file = options()

}


#' Manage hemibrain-FAFB neuron matches
#'
#' @description We can match neurons in the hemibrain data with FAFB neurons (hemibrain->FAFB, hemibrain tab) and
Expand Down Expand Up @@ -1215,7 +1218,8 @@ lm_matches <- function(priority = c("hemibrain","lm"), selected_file = options()
#' @param catmaid.update logical. Whether or not to update \code{flywire.xyz} and \code{flywire.id} columns, based on e CATMAID neuron specified by a \code{skid} column.
#' @param reorder logical. Whether or not to re-write the sheet so that it is ordered by hemilineage.
#' @param nblast if \code{top.nblast} is \code{TRUE} this nblast matrix is used to update the column \code{top.nblast}. If set to \code{NULL} defaults to using \code{hemibrain_nblast}. Columns should be hemibrain neurons, and rows the other data set.
#'
#' @param nblast.hemibrain.catmaid if \code{top.nblast} is \code{TRUE} this nblast matrix is used to update the column \code{top.nblast}. If set to \code{NULL} defaults to using \code{hemibrain_nblast}. Columns should be hemibrain neurons, and rows CATMAID neurons.
#' @param nblast.hemibrain.flywire if \code{top.nblast} is \code{TRUE} this nblast matrix is used to update the column \code{top.nblast}. If set to \code{NULL} defaults to using \code{hemibrain_nblast}. Columns should be hemibrain neurons, and rows flywire neurons.
#' @param ... arguments passed to methods for, for example, \code{neuprintr::neuprint_get_meta} and \code{elmr::fafb_get_meta}.
#'
#' @return \code{NULL}. Updates the master Google sheet.
Expand Down Expand Up @@ -1527,6 +1531,7 @@ fafb_matching_rewrite <- function(selected_file = options()$hemibrainr_matching
n = plyr::rbind.fill(n, n3[,c("skid","ItoLee_Hemilineage", "Hartenstein_Hemilineage", "cell_body_fiber")])
}
matches = tryCatch(hemibrain_matches(selected_file=selected_file), error = function(e) NULL)
matches = subset(matches, ! matches$quality %in% "NBLAST")
if(!is.null(matches)){
n$cell.type = matches[match(n$skid, matches$id),"connectivity.type"]
}else{
Expand Down Expand Up @@ -1604,6 +1609,9 @@ id_okay <- function(x, zero = TRUE, logical = FALSE){
hemibrain_matching_rewrite <- function(ids = NULL,
selected_file = options()$hemibrainr_matching_gsheet,
top.nblast = FALSE,
meta = NULL,
nblast.hemibrain.catmaid = NULL,
nblast.hemibrain.flywire = NULL,
...){
gs = hemibrain_match_sheet(sheet = "hemibrain", selected_file = selected_file)
if(is.null(ids)){
Expand Down Expand Up @@ -1631,22 +1639,21 @@ hemibrain_matching_rewrite <- function(ids = NULL,
meta = meta[order(meta$cell.type),]
meta = meta[order(meta$ItoLee_Hemilineage),]
if(top.nblast){
nblast = tryCatch(hemibrain_nblast('hemibrain-fafb14'), error = function(e) NULL)
if(!is.null(nblast)){
nblast.top =nblast[,match(meta$bodyid,colnames(nblast))]
nblast.hemibrain.catmaid = tryCatch(hemibrain_nblast('hemibrain-fafb14'), error = function(e) NULL)
if(!is.null(nblast.hemibrain.catmaid)){
nblast.top = nblast.hemibrain.catmaid[,match(meta$bodyid,colnames(nblast.hemibrain.catmaid))]
tops = apply(nblast.top,1,function(r) which.max(r))
top = rownames(nblast)[unlist(tops)]
top[!meta$bodyid%in%colnames(nblast)] = NA
meta$nblast.catmaid.top = top
top = rownames(nblast.hemibrain.catmaid)[unlist(tops)]
top[!meta$bodyid%in%colnames(nblast.hemibrain.catmaid)] = NA
meta$catmaid.nblast.top = top
}
nblast = tryCatch(hemibrain_nblast('hemibrain-flywire'), error = function(e) NULL)
fw.neurons = tryCatch(flywire_neurons(), error = function(e) NULL)
if(!is.null(nblast) & !is.null(fw.neurons)){
nblast.top =nblast[,match(meta$bodyid,colnames(nblast))]
nblast.hemibrain.flywire = tryCatch(hemibrain_nblast('hemibrain-flywire'), error = function(e) NULL)
if(!is.null(nblast.hemibrain.flywire) & !is.null(meta)){
nblast.top =nblast.hemibrain.flywire[,match(meta$bodyid,colnames(nblast.hemibrain.flywire))]
tops = apply(nblast.top,1,function(r) which.max(r))
top = rownames(nblast)[unlist(tops)]
top[!meta$bodyid%in%colnames(nblast)] = NA
meta$nblast.flywire.top = fw.neurons[unlist(top),"flywire.xyz"]
top = rownames(nblast.hemibrain.flywire)[unlist(tops)]
top[!meta$bodyid%in%colnames(nblast.hemibrain.flywire)] = NA
meta$flywire.nblast.top = meta[match(unlist(top),meta$flywire.id),"flywire.xyz"]
}
}
if(!identical(gs,meta)){
Expand Down Expand Up @@ -1779,6 +1786,3 @@ id = '%s'; overwrite = '%s'; quality.field = '%s'; match.field = '%s'; initials
# return
selected
}



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