From 1d6b4d83217f131bc2498d2762f7e9721d3f1757 Mon Sep 17 00:00:00 2001
From: alexanderbates <alexander.shakeel.bates@gmail.com>
Date: Tue, 3 Sep 2024 23:16:47 -0400
Subject: [PATCH] Fixed undocumented argument

---
 R/banc-table.R       |  7 +++++++
 R/ids.R              |  3 +++
 R/urls.R             | 22 ++++++++++++++++++++++
 man/banc_latestid.Rd |  4 ++++
 4 files changed, 36 insertions(+)

diff --git a/R/banc-table.R b/R/banc-table.R
index f8c1a95..6957aaf 100644
--- a/R/banc-table.R
+++ b/R/banc-table.R
@@ -372,3 +372,10 @@ banc_update_status <- function(df, update, col = "status", wipe = FALSE){
 #                       chunksize = 100)
 
 
+
+
+
+
+
+
+
diff --git a/R/ids.R b/R/ids.R
index 049f1a7..200cced 100644
--- a/R/ids.R
+++ b/R/ids.R
@@ -114,6 +114,9 @@ banc_islatest <- function(x, timestamp=NULL, ...) {
 #' Find the latest id for a banc root id
 #'
 #' @inheritParams fafbseg::flywire_latestid
+#' @param x a `data.frame` with at least one of: `root_id`, `pt_root_id`, `supervoxel_id` and/or `pt_supervoxel_id`.
+#' Supervoxels will be preferentially used to update the `root_id` column.
+#' Else a vector of `BANC` root IDs.
 #' @param ... Additional arguments passed to \code{\link{flywire_latestid}}
 #'
 #' @export
diff --git a/R/urls.R b/R/urls.R
index e3d67c0..c8a6258 100644
--- a/R/urls.R
+++ b/R/urls.R
@@ -306,3 +306,25 @@ banc_fetch <- function(url, token=banc_token(), ...) {
   else x
 }
 
+# Make a neuroglancer layer with 3D points in it, for synapse review
+banc_annotation_layer <- function(data,
+                                  layer = "sample",
+                                  open = FALSE,
+                                  rawcoords = NA,
+                                  colpal = NULL){
+  #data <- read_csv('/Users/abates/projects/flyconnectome/bancpipeline/tracing/2024-08-12_banc_synapse_sample_v1.csv')
+  #data$pt_position<-data$`Coordinate 1`
+  data$layer <- "synapse_sample"
+  al <- ngl_annotation_layers(data[,c("pt_position", "layer")], rawcoords=rawcoords, colpal=colpal)
+  sc<-fafbseg::ngl_decode_scene(banc_scene())
+  sc2<-sc+al
+  u<-as.character(sc2)
+  su<-banc_shorturl(u)
+  # # Extract annotations!
+  # ngl_annotations(su)
+  if(open){
+    browseURL(u)
+  }else{
+    su
+  }
+}
diff --git a/man/banc_latestid.Rd b/man/banc_latestid.Rd
index 4de3168..5784120 100644
--- a/man/banc_latestid.Rd
+++ b/man/banc_latestid.Rd
@@ -30,6 +30,10 @@ dataset.}
 of}
 
 \item{...}{Additional arguments passed to \code{\link{flywire_latestid}}}
+
+\item{x}{a \code{data.frame} with at least one of: \code{root_id}, \code{pt_root_id}, \code{supervoxel_id} and/or \code{pt_supervoxel_id}.
+Supervoxels will be preferentially used to update the \code{root_id} column.
+Else a vector of \code{BANC} root IDs.}
 }
 \description{
 Find the latest id for a banc root id