Namespace fixes

DESCRIPTION

@@ -37,7 +37,7 @@ Suggests:
     reticulate,
     readobj,
     Rvcg,
-    Morpo,
+    Morpho,
     usethis,
     rmarkdown,
     spelling,

R/cave-tables.R

@@ -75,31 +75,31 @@ banc_nuclei <- function (rootids = NULL,
     }
     if (nrow(nuclei) == 0)
       return(nuclei)
-    nuclei <- nuclei %>% right_join(data.frame(pt_root_id = as.integer64(rootids)),
+    nuclei <- nuclei %>% dplyr::right_join(data.frame(pt_root_id = as.integer64(rootids)),
                                     by = "pt_root_id") %>% select(colnames(nuclei))
     if (length(rootids) < 200) {
       nuclei
     }
     else {
-      nuclei %>% mutate(pt_root_id = flywire_updateids(.data$pt_root_id,
+      nuclei %>% dplyr::mutate(pt_root_id = flywire_updateids(.data$pt_root_id,
                                                        svids = .data$pt_supervoxel_id))
     }
   }else {
     nid <- paste(nucleus_ids, collapse = ",")
     nidq <- reticulate::py_eval(sprintf("{\"id\": [%s]}",
                                        nid), convert = F)
-    nuclei <- flywire_cave_query(table = nucleus_table_name(),
+    nuclei <- flywire_cave_query(table = table,
                                 filter_in_dict = nidq, ...)
-    nuclei %>% right_join(data.frame(id = nucleus_ids), by = "id") %>%
-      select(colnames(nuclei))
+    nuclei %>% dplyr::right_join(data.frame(id = nucleus_ids), by = "id") %>%
+      dplyr::select(colnames(nuclei))
   }
   res
   #  apply coordinate transform
   # res <- standard_nuclei(res)
   if (isFALSE(rawcoords))
     res
   else {
-    res %>% dplyr::mutate(across(ends_with("position"), function(x) xyzmatrix2str(flywire_nm2raw(x))))
+    res %>% dplyr::mutate(dplyr::across(dplyr::ends_with("position"), function(x) nat::xyzmatrix2str(flywire_nm2raw(x))))
   }
 }
 

R/meshes.R

@@ -45,7 +45,7 @@ banc_read_nuclei_mesh <- function(ids, lod = 1L, savedir=NULL,  method=c('vf', '
 
 #' Subset points to be in the brain or in the VNC
 #'
-#' @param x an object with 3d points to be subsetted, e.g. an xyz matrix, a \code{neuron}, \cpode{neuronlist} or a \code{mesh3d} object.
+#' @param x an object with 3d points to be subsetted, e.g. an xyz matrix, a \code{neuron}, \code{neuronlist} or a \code{mesh3d} object.
 #' Points must be in native BANC space, i.e. plottable inside \code{banc.surf}.
 #' @param invert if \code{FALSE} returns brain points, if \code{TRUE} returns VNC points.
 #'
@@ -67,17 +67,17 @@ banc_decapitate <- function(x, invert = FALSE, reference = "BANC"){
   v2 <- c(1e10,y.cut,0)
   v3 <- c(0,y.cut,1e10)
   if (reference!="BANC"){
-    v1 <- xform_brain(v1, sample = "BANC", reference = reference)
-    v2 <- xform_brain(v2, sample = "BANC", reference = reference)
-    v3 <- xform_brain(v3, sample = "BANC", reference = reference)
+    v1 <- nat.templatebrains::xform_brain(v1, sample = "BANC", reference = reference)
+    v2 <- nat.templatebrains::xform_brain(v2, sample = "BANC", reference = reference)
+    v3 <- nat.templatebrains::xform_brain(v3, sample = "BANC", reference = reference)
     y.cut <- v1[,2]
   }
   ismesh <- any(class(x[[1]]), class(x)) %in% "mesh3d"
   if(!ismesh & any(class(x)%in%c("neuron","neuronlist","mesh3d"))){
     if (invert){
-      z <- subset(x,y<y.cut)
+      z <- subset(x,x$y<y.cut)
     }else{
-      z <- subset(x,y>y.cut)
+      z <- subset(x,x$y>y.cut)
     }
   }else if (ismesh){
     if (any(class(x)=="mesh3d")){

R/synapses.R

@@ -65,7 +65,7 @@ banc_all_synapses <- function(path = "gs://zetta_lee_fly_cns_001_synapse/240623_
   )
 
   # Are we just sampling or going for the full thing?
-  if(!is.null(nrows)){
+  if(!is.null(n_max)){
     syns <- readr::read_csv(file=path, col_types = col.types, lazy = TRUE, n_max = n_max)
     return(syns)
   }else if (!table_exists|overwrite){
@@ -81,7 +81,7 @@ banc_all_synapses <- function(path = "gs://zetta_lee_fly_cns_001_synapse/240623_
     # If the table already exists, it will be overwritten
     DBI::dbWriteTable(con, "synapses", df, overwrite = TRUE)
     DBI::dbDisconnect(con)
-    message("Added tab synapses, nrows: ", nrow(syns))
+    message("Added tab synapses, no. rows: ", nrow(syns))
   }
 
   # Read