Merge pull request #428 from natverse/feature/more-elmr

Remaining items to move from elmr

NAMESPACE

@@ -117,6 +117,7 @@ S3method(plot3d,dotprops)
 S3method(plot3d,hxsurf)
 S3method(plot3d,neuron)
 S3method(plot3d,neuronlist)
+S3method(plot3d,ngraph)
 S3method(pointsinside,default)
 S3method(potential_synapses,dotprops)
 S3method(potential_synapses,neuron)
@@ -364,6 +365,7 @@ importFrom(igraph,V)
 importFrom(igraph,add.edges)
 importFrom(igraph,as.directed)
 importFrom(igraph,as.undirected)
+importFrom(igraph,as_edgelist)
 importFrom(igraph,decompose.graph)
 importFrom(igraph,degree)
 importFrom(igraph,delete.vertices)
@@ -386,10 +388,15 @@ importFrom(nat.utils,RunCmdForNewerInput)
 importFrom(nat.utils,is.gzip)
 importFrom(nat.utils,makelock)
 importFrom(nat.utils,removelock)
+importFrom(rgl,arrow3d)
 importFrom(rgl,par3d)
 importFrom(rgl,plot3d)
+importFrom(rgl,points3d)
+importFrom(rgl,pop3d)
 importFrom(rgl,rotationMatrix)
 importFrom(rgl,scaleMatrix)
+importFrom(rgl,spheres3d)
+importFrom(rgl,text3d)
 importFrom(stats,approx)
 importFrom(stats,dnorm)
 importFrom(stats,na.omit)

R/nat-data.R

@@ -74,9 +74,9 @@ NULL
 
 #' Olfactory Projection Neuron reconstructed from EM data
 #'
-#' A DL1 olfactory projection neuuronobject traced in CATMAID from the FAFB
+#' A DL1 olfactory projection neuron object traced in CATMAID from the FAFB
 #' whole brain EM volume. This has a complex morphology that makes a good test
-#' for pruning and simplifcation strategies.
+#' for pruning and simplification strategies.
 #'
 #' @format A \code{neuron} object with additional class \code{catmaidneuron}
 #' @source \url{http://www.diamondse.info/}

R/neuron-plot.R

@@ -634,3 +634,60 @@ check_plotengine <- function(plotengine) {
                   '"', plotengine, '"',
                   "\nSee ?plot3d.neuronlist for details.", call.=FALSE))
 }
+
+#' Plot 3d representation of neuron (ngraph) with directed edges
+#'
+#' @param x A \code{\link{ngraph}} object
+#' @param type They type of arrows (lines by default, see \code{\link{arrow3d}}
+#'   for details).
+#' @param soma radius of soma (or \code{FALSE} to suppress plotting)
+#' @param labels Whether to label nodes/all points with their raw index (not
+#'   id)
+#' @param ... Additional arguments passed to \code{\link{arrow3d}}
+#'
+#' @export
+#'
+#' @importFrom igraph as_edgelist V
+#' @importFrom rgl arrow3d par3d spheres3d text3d points3d pop3d
+#' @examples
+#' plot3d(as.ngraph(Cell07PNs[[1]]), labels='nodes')
+plot3d.ngraph <- function(x, type='lines', soma=1, 
+                          labels=c('none', "nodes","all"), ...) {
+  labels=match.arg(labels)
+  el=igraph::as_edgelist(x, names=F)
+  xyz=xyzmatrix(x)
+
+  draw_edge <- function(edge, ...) {
+    e1=edge[1]
+    e2=edge[2]
+    if(e1 == e2) return()
+    p1=xyz[e1,]
+    p2=xyz[e2,]
+    if(any(is.na(c(p1,p2))) || all(p1==p2)) {
+      message("Bad edge: ", edge)
+      return()
+    }
+    # cat(edge,"\n")
+    arrow3d(xyz[edge[1],], xyz[edge[2],], type=type, ...)
+  }
+  # add points at each vertex so that scene dimensions
+  # are correctly set for arrows
+  pp=points3d(xyz, size=1)
+  op=par3d(skipRedraw=T)
+  on.exit(par3d(op))
+  on.exit(pop3d(id=pp), add = TRUE, after = TRUE)
+  apply(el, 1, draw_edge, ...)
+  rp=rootpoints(x)
+  if(isTRUE(all.equal(soma, FALSE))) {
+    # don't plot
+  } else spheres3d(xyz[rp,, drop=F], col='magenta', radius=soma)
+  if(labels!='none') {
+    all_points=igraph::V(x)
+    pointsel <- if(isTRUE(labels=='all')) {
+      all_points
+    } else {
+      unique(c(branchpoints(x), rootpoints(x), endpoints(x)))
+    }
+    text3d(xyz[pointsel,],texts = pointsel)
+  }
+}

R/ngraph.R

@@ -57,7 +57,7 @@
 #' @family neuron
 #' @seealso \code{\link{igraph}}, \code{\link[igraph]{set.vertex.attribute}},
 #'   \code{\link{subset.neuron}} for example of graph-based manipulation of a
-#'   neuron.
+#'   neuron, \code{\link{plot3d.ngraph}}
 #' @export
 #' @importFrom igraph V<-
 #' @examples

_pkgdown.yml

@@ -163,6 +163,7 @@ reference:
       - plot3d.hxsurf
       - plot3d.neuron
       - plot3d.cmtkreg
+      - plot3d.ngraph
   - title: 3D Interaction with Objects
     desc: Functions to review, identify, and modify objects by interactive selection in RGL windows.
     contents: