Updated banc_decapitate and ggplot util function for neurons

NAMESPACE

@@ -1,7 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(banc_decapitate,data.frame)
+S3method(banc_decapitate,matrix)
+S3method(banc_decapitate,mesh3d)
+S3method(banc_decapitate,neuron)
+S3method(banc_decapitate,neuronlist)
+S3method(ggplot2_neuron_path,neuron)
+S3method(ggplot2_neuron_path,neuronlist)
 export(banc_all_synapses)
 export(banc_backbone_proofread)
+export(banc_brain_neuropil.surf)
 export(banc_cave_client)
 export(banc_cave_query)
 export(banc_cave_tables)
@@ -10,11 +18,14 @@ export(banc_cell_info)
 export(banc_cellid_from_segid)
 export(banc_change_log)
 export(banc_decapitate)
+export(banc_front_view)
 export(banc_ids)
 export(banc_islatest)
 export(banc_latestid)
 export(banc_leaves)
+export(banc_neck_connective.surf)
 export(banc_neck_connective_neurons)
+export(banc_neuropil.surf)
 export(banc_nm2raw)
 export(banc_nuclei)
 export(banc_partner_summary)
@@ -24,16 +35,21 @@ export(banc_raw2nm)
 export(banc_read_l2dp)
 export(banc_read_l2skel)
 export(banc_read_neuroglancer_mesh)
+export(banc_read_neuron_meshes)
 export(banc_read_nuclei_mesh)
 export(banc_rootid)
 export(banc_scene)
 export(banc_segid_from_cellid)
 export(banc_set_token)
+export(banc_side_view)
+export(banc_view)
+export(banc_vnc_neuropil.surf)
+export(banc_vnc_view)
 export(banc_voxdims)
 export(banc_xyz2id)
 export(choose_banc)
 export(dr_banc)
-export(banc_read_neuron_meshes)
+export(ggplot2_neuron_path)
 export(with_banc)
 import(bit64)
 import(fafbseg)

R/ggplot2.R

@@ -0,0 +1,140 @@
+banc_neuron_comparison_plot <- function(neuron1, neuron2,
+                                        filename =  NULL,
+                                        width = 8, height = 6) {
+
+  # Get 3D spatial points
+  glist <- list()
+  for(view in names(banc_rotation_matrices)){
+
+    # Choose mesh
+    if(view=="front"){
+      mesh <- banc_brain_neuropil.surf
+      decaptitate <- "brain"
+    }else if(view=="vnc"){
+      mesh <- banc_vnc_neuropil.surf
+      decaptitate <- "vnc"
+    }else{
+      mesh <- banc_neuropil.surf
+      decaptitate <- "none"
+    }
+
+    # Get 3D points
+    vertices <- nat::xyzmatrix(mesh)
+    if(decaptitate=="brain"){
+      neuron_pruned1 <- banc_decapitate(neuron1, invert = TRUE)
+      neuron_pruned2 <- banc_decapitate(neuron2, invert = TRUE)
+    }else if(decaptitate=="vnc"){
+      neuron_pruned1 <- banc_decapitate(neuron1, invert = FALSE)
+      neuron_pruned2 <- banc_decapitate(neuron2, invert = FALSE)
+    }else{
+      neuron_pruned1=neuron1
+      neuron_pruned2=neuron2
+    }
+
+    # Rotate mesh
+    rotation_matrix <- banc_rotation_matrices[[view]]
+    rotated_vertices <- as.data.frame(t(rotation_matrix[,1:3] %*% t(as.matrix(vertices))))
+    rotated_vertices <- rotated_vertices[,-4]
+    colnames(rotated_vertices) <- c("X","Y","Z")
+
+    # Process neuron 1
+    edges_df1 <- ggplot2_neuron_path(neuron_pruned1, rotation_matrix=rotation_matrix)
+
+    # Process neuron 2
+    edges_df2 <- ggplot2_neuron_path(neuron_pruned2, rotation_matrix=rotation_matrix)
+
+    # Create the plot
+    p <- ggplot() +
+      geom_point(data = rotated_vertices, aes(x = X, y = Y), color = "grey", size = 1, alpha = 0.05) +
+      #scale_color_gradient(low = "grey100", high = "grey50") +
+      ggnewscale::new_scale_colour() +
+      geom_path(data = edges_df1, aes(x = X, y = Y, color = Z, group = group), alpha = 0.5, linewidth = 0.5) +
+      scale_color_gradient(low = "navy", high = "cyan") +
+      ggnewscale::new_scale_colour() +
+      geom_path(data = edges_df2, aes(x = X, y = Y, color = Z, group = group), alpha = 0.5, linewidth = 0.5) +
+      scale_color_gradient(low = "coral", high = "darkred") +
+      theme_minimal() +
+      coord_equal() +
+      labs(title = view) +
+      theme(legend.position = "none") +
+      theme(axis.title.x=element_blank(),
+            axis.text.x=element_blank(),
+            axis.ticks.x=element_blank(),
+            axis.title.y=element_blank(),
+            axis.text.y=element_blank(),
+            axis.ticks.y=element_blank())
+
+    # Add to list
+    glist[[view]] <- p
+  }
+
+  # Arrange plot
+  g <- gridExtra::grid.arrange(glist[["main"]], glist[["side"]], glist[["front"]], glist[["vnc"]], ncol = 2,
+                               layout_matrix = rbind(c(1,1,1,2,2,3,3,3,3),
+                                                     c(1,1,1,2,2,3,3,3,3),
+                                                     c(1,1,1,2,2,4,4,4,4),
+                                                     c(1,1,1,2,2,4,4,4,4)
+                               ))
+  if(filename){
+    ggsave(filename, plot = p, width = width, height = height)
+    invisible()
+  }else{
+    plot(g)
+  }
+}
+
+#' Convert Neuron Objects to ggplot2-Compatible Path Data
+#'
+#' @description
+#' This function converts 'neuron' or 'neuronlist' objects, which represent 3D
+#' points linked by lines in space, into data frames that describe paths
+#' compatible with ggplot2's geom_path.
+#'
+#' @param x A 'neuron' or 'neuronlist' object to be converted.
+#' @param rotation_matrix An optional 4x4 rotation matrix to apply to the neuron coordinates.
+#' @param ... Additional arguments passed to methods.
+#'
+#' @return A data frame with columns X, Y, Z, and group, where each group
+#' represents a continuous path in the neuron.
+#'
+#' @export
+ggplot2_neuron_path <- function(x, rotation_matrix = NULL, ...) UseMethod('ggplot2_neuron_path')
+
+#' @rdname ggplot2_neuron_path
+#' @method ggplot2_neuron_path neuron
+#' @export
+ggplot2_neuron_path.neuron <- function(x, rotation_matrix = NULL){
+  x$d <- x$d[order(x$d$Parent),]
+  x$d <- x$d[order(x$d$PointNo),]
+  npoints <- nat::xyzmatrix(x)
+  edges_df <- data.frame()
+  if(!is.null(rotation_matrix)){
+    npoints <- as.data.frame(t(rotation_matrix[,1:3] %*% t(xyzmatrix(npoints))))
+    npoints <- npoints[,-4]
+    colnames(npoints) <- c("X","Y","Z")
+  }
+  ss <-nat::seglist(x)
+  seglist <- ss[[1]]$SegList
+  for(s in 1:length(seglist)){
+    g <- npoints[seglist[[s]],]
+    g$group <- s
+    edges_df <- rbind(edges_df,g)
+  }
+  edges_df
+}
+
+#' @rdname ggplot2_neuron_path
+#' @method ggplot2_neuron_path neuronlist
+#' @export
+ggplot2_neuron_path.neuronlist <- function(x, rotation_matrix = NULL){
+  ll <- lapply(x, ggplot2_neuron_path, rotation_matrix = rotation_matrix, ...)
+  max.group <- 0
+  for(i in 1:length(ll)){
+    ll[[i]]$group <- ll[[i]]$group + max.group
+    max.group <- max(ll[[i]]$group, na.rm = TRUE)
+  }
+  do.call(rbind, ll)
+}
+
+
+

R/meshes.R

@@ -61,47 +61,54 @@ banc_read_nuclei_mesh <- function(ids, lod = 1L, savedir=NULL,  method=c('vf', '
 #' plot3d(m.brain, col = "cyan")
 #' plot3d(banc.surf, col = "grey", alpha = 0.1)
 #' }
-banc_decapitate <- function(x, invert = FALSE, reference = "BANC"){
-  y.cut <- 5e+05
-  v1 <- c(0,y.cut,0)
-  v2 <- c(1e10,y.cut,0)
-  v3 <- c(0,y.cut,1e10)
-  if (reference!="BANC"){
-    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]
+banc_decapitate<-function(x, y.cut = 5e+05, invert = FALSE, ...) UseMethod('banc_decapitate')
+
+#' @export
+#' @rdname banc_decapitate
+banc_decapitate.neuron <- function(x, y.cut = 5e+05, invert = FALSE, ...){
+  z <- as.data.frame(nat::xyzmatrix(x))
+  rownames(z) <- x$d$PointNo
+  z <- subset(z,z$Y<y.cut)
+  nat::prune_vertices(x, verticestoprune = rownames(z), invert = invert, ...)
+}
+
+#' @export
+#' @rdname banc_decapitate
+banc_decapitate.neuronlist <- function(x, y.cut = 5e+05, invert = FALSE, ...){
+  nat::nlapply(x, banc_decapitate, y.cut = y.cut, invert = invert, ...)
+}
+
+#' @export
+#' @rdname banc_decapitate
+banc_decapitate.matrix <- function(x, y.cut = 5e+05, invert = FALSE){
+  z <- nat::xyzmatrix(x)
+  if(invert){
+    z[z[,2]<y.cut,]
+  }else{
+    z[z[,2]>y.cut,]
   }
-  ismesh <- any( c(class(x[[1]]), class(x)) %in% "mesh3d")
-  if(!ismesh & any(class(x)%in%c("neuron","neuronlist","mesh3d"))){
-    if (invert){
-      z <- subset(x,x$y<y.cut)
-    }else{
-      z <- subset(x,x$y>y.cut)
-    }
-  }else if (ismesh){
-    if (any(class(x)=="mesh3d")){
-      z <- Morpho::cutMeshPlane(x,
-                                v1=v1, v2=v2, v3=v3,
-                                normal = NULL, keep.upper = invert)
-    }else if (any(class(x)=="neuronlist")){
-      z <- nat::nlapply(x, Morpho::cutMeshPlane,
-                        v1=v1, v2=v2, v3=v3,
-                        normal = NULL, keep.upper = invert)
-    }else{
-      z <- lapply(x, Morpho::cutMeshPlane,
-                  v1=v1, v2=v2, v3=v3,
-                  normal = NULL, keep.upper = invert)
-    }
+}
+
+#' @export
+#' @rdname banc_decapitate
+banc_decapitate.data.frame <- function(x, y.cut = 5e+05, invert = FALSE){
+  z <- nat::xyzmatrix(x)
+  if(invert){
+    x[z[,2]<y.cut,]
   }else{
-    ydim <- intersect(colnames(x),c("Y","y"))[[1]]
-    if (invert){
-      z <- x[x[,ydim]<y.cut,]
-    }else{
-      z <- x[x[,ydim]>y.cut,]
-    }
+    x[z[,2]>y.cut,]
   }
-  z
+}
+
+#' @export
+#' @rdname banc_decapitate
+banc_decapitate.mesh3d <- function(x, y.cut = 5e+05, invert = FALSE, ...){
+  v1 <- c(0,y.cut,0)
+  v2 <- c(1e10,y.cut,0)
+  v3 <- c(0,y.cut,1e10)
+  Morpho::cutMeshPlane(x,
+                      v1=v1, v2=v2, v3=v3,
+                      normal = NULL, keep.upper = invert)
 }
 
 #' Read BANC euroglancer meshes, e.g., ROI meshes