Merge branch 'main' of github.com:flyconnectome/bancr

NAMESPACE

@@ -8,7 +8,10 @@ S3method(banc_decapitate,mesh3d)
 S3method(banc_decapitate,neuron)
 S3method(banc_decapitate,neuronlist)
 S3method(geom_neuron,"NULL")
+S3method(geom_neuron,data.frame)
 S3method(geom_neuron,hxsurf)
+S3method(geom_neuron,list)
+S3method(geom_neuron,matrix)
 S3method(geom_neuron,mesh3d)
 S3method(geom_neuron,neuron)
 S3method(geom_neuron,neuronlist)

R/ggplot2.R

@@ -391,6 +391,51 @@ geom_neuron.NULL <- function(x = NULL, rotation_matrix = NULL, root = 3, low = "
   )
 }
 
+#' @rdname geom_neuron
+#' @method geom_neuron list
+#' @export
+geom_neuron.list <- function(x = NULL, rotation_matrix = NULL, root = 3, low = "navy", high = "turquoise",
+                             stat = "identity", position = "identity", na.rm = FALSE, show.legend = NA,
+                             inherit.aes = FALSE, ...) {
+
+  if(length(x)){
+    geom_neuron.neuronlist(x=x, rotation_matrix=rotation_matrix, low=low, high=high,
+                       stat=stat, position=position, na.rm=na.rm, show.legend=show.legend, inherit.aes=inherit.aes,
+                       ...)
+  }else{
+    geom_neuron.NULL(x = x, ...)
+  }
+}
+
+#' @rdname geom_neuron
+#' @method geom_neuron matrix
+#' @export
+geom_neuron.matrix <- function(x = NULL, rotation_matrix = NULL, root = 3, low = "navy", high = "turquoise",
+                             stat = "identity", position = "identity", na.rm = FALSE, show.legend = NA,
+                             inherit.aes = FALSE, ...) {
+  x<- as.data.frame(nat::xyzmatrix(x))
+  list(
+    ggplot2::geom_point(data = x, mapping = ggplot2::aes(x = .data$X, y = .data$Y, color = .data$Z),
+                        size = root,  ...),
+    ggplot2::scale_color_gradient(low = low, high = high),
+    ggnewscale::new_scale_colour()
+  )
+}
+
+#' @rdname geom_neuron
+#' @method geom_neuron data.frame
+#' @export
+geom_neuron.data.frame <- function(x = NULL, rotation_matrix = NULL, root = 3, low = "navy", high = "turquoise",
+                               stat = "identity", position = "identity", na.rm = FALSE, show.legend = NA,
+                               inherit.aes = FALSE, ...) {
+  geom_neuron.matrix(x, rotation_matrix = rotation_matrix, root = root,
+                     low = low, high = high,
+                     stat = stat, position = position,
+                     na.rm = FALSE, show.legend = NA,
+                     inherit.aes = FALSE,
+                     ...)
+}
+
 #' Create a ggplot2 Visualisation of Neuron Objects
 #'
 #' @description

R/xform.R

@@ -547,3 +547,18 @@ banc_mirror <- function(x,
   return(x)
 
 }
+
+# hidden, for now
+banc_lr_position <- function (x, units = c("nm", "um", "raw"), group = FALSE, ...) {
+  xyz = xyzmatrix(x)
+  xyzt = banc_mirror(xyz, units = units, ...)
+  lrdiff = xyzt[, 1] - xyz[, 1]
+  if (group) {
+    if (!is.neuronlist(x))
+      stop("I only know how to group results for neuronlists")
+    df = data.frame(lrdiff = lrdiff, id = rep(names(x), nvertices(x)))
+    dff = summarise(group_by(df, .data$id), lrdiff = mean(lrdiff))
+    lrdiff = dff$lrdiff[match(names(x), dff$id)]
+  }
+  lrdiff
+}