Merge pull request #41 from fmlove/dev

Improvements to find_glomeruli for better mPN handling

Author: fmlove

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tracerutils
 Type: Package
 Title: Utilities for EM Neuron Tracers
-Version: 0.6.1
+Version: 0.7.0
 Authors@R: person("Fiona", "Love", email = "fl299@cam.ac.uk", role = c("aut", "cre"))
 Description: Helpful functions for handling neurons traced from EM volumes.
     Interacts with CATMAID and NBLAST.

R/3D_plots.R

@@ -24,7 +24,6 @@ plot_catmaid <- function(skid, volumes = NULL, ncol = NULL, vcol = NULL, valpha
   if (!is.null(volumes)){
     plotVolumes(volumes, vcol, valpha)
   }
-
   invisible(neurons)#returned in case you want to do anything else with them, but not printed to console
 }
 
@@ -68,7 +67,7 @@ plotVolumes <- function(volumes, vcol, valpha, pid = 1){#plot multiple neuropil
     if (length(valpha) < length(volumes)) valpha = rep(valpha, length.out = length(volumes))
   }
   else{
-    valpha = rep(0.5, length(volumes))
+    valpha = rep(0.1, length(volumes))
   }
 
 

R/utils.R

@@ -118,18 +118,23 @@ simple_catmaid_url <- function(dfrow, skid, sid0 = 5, zoom = 0, conn = FALSE, tr
 #' Note that annotations of the form \bold{glomerulus \emph{X} right|left} are not considered.
 #'
 #' @param skids Required; an \code{integer} or \code{character} vector of skeleton IDs
+#' @param exclude Optional; a vector of glomeruli to exclude (in the format \bold{\emph{X}} for \bold{glomerulus \emph{X}}, or the full annotation for \bold{unknown glomerulus \emph{N}})
 #' @return A \code{character} vector of glomeruli names
 #'
 #' @export
 #'
-find_glomeruli <- function(skids){
+find_glomeruli <- function(skids, exclude = NULL){
   annotations = catmaid::catmaid_get_annotations_for_skeletons(unique(skids))
   annotations.glom = annotations[grepl("^glomerulus [A-Za-z0-9]+$", annotations$annotation),]
   annotations.glom$glom = sapply(annotations.glom$annotation, function(a){ sub("glomerulus ", "", a) })
   annotations.unknown_glom = annotations[grepl("^unknown glomerulus \\d+$", annotations$annotation),]
+
+  annotations.glom = annotations.glom[!annotations.glom$glom %in% exclude,]
+  annotations.unknown_glom = annotations.unknown_glom[!annotations.unknown_glom$annotation %in% exclude,]
+
   glomeruli = sapply(skids, function(s){
-    s.glom = paste(annotations.glom[annotations.glom$skid == s, "glom"], sep = "", collapse = "/")
-    s.unknown_glom = paste(annotations.unknown_glom[annotations.unknown_glom$skid == s, "annotation"], sep = "", collapse = "/")
+    s.glom = paste(sort(unlist(annotations.glom[annotations.glom$skid == s, "glom"])), sep = "", collapse = "/")
+    s.unknown_glom = paste(sort(unlist(annotations.unknown_glom[annotations.unknown_glom$skid == s, "annotation"])), sep = "", collapse = "/")
     if(nchar(s.glom) > 0){
       s.glom
     }