Merge pull request #432 from natverse/feature/plotly_grids_labels

Updated parameter for toggling grid lines in plotly

R/cmtkreg.R

@@ -144,7 +144,7 @@ cmtkreg.filetype <- function(x) {
 #' }
 #' @importFrom rgl plot3d
 #' @export
-plot3d.cmtkreg <- function(x, ..., plotengine = getOption('nat.plotengine')) {
+plot3d.cmtkreg <- function(x, ..., gridlines = FALSE, plotengine = getOption('nat.plotengine')) {
   plotengine <- check_plotengine(plotengine)
   if (plotengine == 'plotly') {
     psh <- openplotlyscene()$plotlyscenehandle
@@ -172,8 +172,15 @@ plot3d.cmtkreg <- function(x, ..., plotengine = getOption('nat.plotengine')) {
     psh <- psh %>% 
       plotly::add_trace(data = plotdata, x = ~X, y = ~Y , z = ~Z,
         hoverinfo = "none",type = 'scatter3d', mode = 'markers',
-        opacity = opacity, marker=list(color = 'black', size = 3)) %>% 
-      plotly::layout(showlegend = FALSE, scene=list(camera=.plotly3d$camera))
+        opacity = opacity, marker=list(color = 'black', size = 3))
+
+    psh <- psh %>% plotly::layout(showlegend = FALSE, scene=list(camera=.plotly3d$camera))
+    if(gridlines == FALSE){
+      psh <- psh %>% plotly::layout(scene = list(xaxis=.plotly3d$xaxis,
+                                                 yaxis=.plotly3d$yaxis,
+                                                 zaxis=.plotly3d$zaxis))
+    }
+
     assign("plotlyscenehandle", psh, envir=.plotly3d)
     psh
   }

R/dotprops.R

@@ -324,7 +324,8 @@ all.equal.dotprops<-function(target, current, check.attributes=FALSE,
 #' }
 plot3d.dotprops<-function(x, scalevecs=1.0, alpharange=NULL, color='black',
                           PlotPoints=FALSE, PlotVectors=TRUE, UseAlpha=FALSE, 
-                          ..., plotengine = getOption('nat.plotengine')){
+                          ..., gridlines = FALSE,
+                          plotengine = getOption('nat.plotengine')){
   # rgl's generic plot3d will dispatch on this
   if (!is.null(alpharange))
     x=subset(x,x$alpha<=alpharange[2] & x$alpha>=alpharange[1])
@@ -379,8 +380,14 @@ plot3d.dotprops<-function(x, scalevecs=1.0, alpharange=NULL, color='black',
   if (plotengine == 'rgl'){
     invisible(rlist)
   } else {
-    psh <- psh %>% 
-      plotly::layout(showlegend = FALSE, scene=list(camera=.plotly3d$camera))
+
+    psh <- psh %>% plotly::layout(showlegend = FALSE, scene=list(camera=.plotly3d$camera))
+    if(gridlines == FALSE){
+      psh <- psh %>% plotly::layout(scene = list(xaxis=.plotly3d$xaxis,
+                                                 yaxis=.plotly3d$yaxis,
+                                                 zaxis=.plotly3d$zaxis))
+    }
+
     assign("plotlyscenehandle", psh, envir=.plotly3d)
     psh
   }

R/hxsurf.R

@@ -376,7 +376,7 @@ write.hxsurf <- function(surf, filename) {
 #' plot3d(MBL.surf, alpha=0.3, 
 #'   materials=grep("VL", MBL.surf$RegionList, value = TRUE, invert = TRUE))
 #' }
-plot3d.hxsurf<-function(x, materials=NULL, col=NULL, ...,
+plot3d.hxsurf<-function(x, materials=NULL, col=NULL, gridlines = FALSE, ...,
                         plotengine = getOption('nat.plotengine')){
   plotengine <- check_plotengine(plotengine)
   if (plotengine == 'rgl'){
@@ -427,9 +427,12 @@ plot3d.hxsurf<-function(x, materials=NULL, col=NULL, ...,
   if (plotengine == 'rgl'){
       invisible(rlist)
   } else {
-    psh <- psh %>% 
-      plotly::layout(showlegend = FALSE,
-                     scene=list(camera=.plotly3d$camera))
+    psh <- psh %>% plotly::layout(showlegend = FALSE, scene=list(camera=.plotly3d$camera))
+    if(gridlines == FALSE){
+      psh <- psh %>% plotly::layout(scene = list(xaxis=.plotly3d$xaxis,
+                                                 yaxis=.plotly3d$yaxis,
+                                                 zaxis=.plotly3d$zaxis))
+    }
     assign("plotlyscenehandle", psh, envir=.plotly3d)
     psh
   }

R/neuron-plot.R

@@ -59,6 +59,7 @@
 plot3d.neuron<-function(x, WithLine=TRUE, NeuronNames=FALSE, WithNodes=TRUE, 
                         WithAllPoints=FALSE, WithText=FALSE, PlotSubTrees=TRUE, 
                         add=TRUE, col=NULL, soma=FALSE, ...,
+                        gridlines = FALSE,
                         plotengine = getOption('nat.plotengine')){
   plotengine <- check_plotengine(plotengine)
   if (!add)
@@ -212,8 +213,13 @@ plot3d.neuron<-function(x, WithLine=TRUE, NeuronNames=FALSE, WithNodes=TRUE,
   if (plotengine == 'rgl'){
     invisible(rglreturnlist)
   } else{
-    psh <- psh %>% 
-      plotly::layout(showlegend = FALSE, scene=list(camera=.plotly3d$camera))
+    psh <- psh %>% plotly::layout(showlegend = FALSE, scene=list(camera=.plotly3d$camera))
+    if(gridlines == FALSE){
+      psh <- psh %>% plotly::layout(scene = list(xaxis=.plotly3d$xaxis,
+                                                 yaxis=.plotly3d$yaxis,
+                                                 zaxis=.plotly3d$zaxis))
+    }
+
     assign("plotlyscenehandle", psh, envir=.plotly3d)
     psh
   }
@@ -546,7 +552,7 @@ plot.neuron <- function(x, WithLine=TRUE, WithNodes=TRUE, WithAllPoints=FALSE,
 #' }
 #' 
 plot3d.boundingbox <- function(x, col='black', 
-                               plotengine = getOption('nat.plotengine'), ...) {
+                               gridlines = FALSE, plotengine = getOption('nat.plotengine'), ...) {
   plotengine <- check_plotengine(plotengine)
   pts <- matrix(c(
   c(x[1, 1], x[1, 2], x[1, 3]),
@@ -580,6 +586,11 @@ plot3d.boundingbox <- function(x, col='black',
         x = ~X, y = ~Y , z = ~Z, 
         hoverinfo = "none", type = 'scatter3d', mode = 'lines',
         opacity = opacity, line=list(color = col, width = width))
+    if(gridlines == FALSE){
+      psh <- psh %>% plotly::layout(scene = list(xaxis=.plotly3d$xaxis,
+                                                 yaxis=.plotly3d$yaxis,
+                                                 zaxis=.plotly3d$zaxis))
+    }
     .plotly3d$plotlyscenehandle <- psh
     psh
   }

R/neuronlist.R

@@ -607,6 +607,8 @@ nmapply<-function(FUN, X, ..., MoreArgs = NULL, SIMPLIFY = FALSE,
 #' @param WithNodes Whether to plot points for end/branch points. Default: 
 #'   \code{FALSE}.
 #' @param ... options passed on to plot3d (such as colours, line width etc)
+#' @param gridlines Whether to display gridlines when using plotly as the backend plotting
+#' engine (default: \code{FALSE})
 #' @param SUBSTITUTE Whether to \code{substitute} the expressions passed as 
 #'   arguments \code{subset} and \code{col}. Default: \code{TRUE}. For expert 
 #'   use only, when calling from another function.
@@ -658,6 +660,7 @@ plot3d.neuronlist<-function(x, subset=NULL, col=NULL, colpal=rainbow,
                             skipRedraw=ifelse(interactive(), 200L, TRUE),
                             WithNodes=FALSE, soma=FALSE, ..., 
                             SUBSTITUTE=TRUE, 
+                            gridlines = FALSE,
                             plotengine = getOption('nat.plotengine')){
   plotengine <- check_plotengine(plotengine)
   # Handle Subset
@@ -691,7 +694,7 @@ plot3d.neuronlist<-function(x, subset=NULL, col=NULL, colpal=rainbow,
     }
   }
 
-  rval=mapply(plot3d, x, plotengine = plotengine,
+  rval=mapply(plot3d, x, plotengine = plotengine, gridlines = gridlines,
               col=cols, soma=soma, ..., 
               MoreArgs = list(WithNodes=WithNodes), SIMPLIFY=FALSE)
   if(plotengine == 'plotly'){
@@ -735,8 +738,13 @@ plot3d.neuronlist<-function(x, subset=NULL, col=NULL, colpal=rainbow,
       attr(rval,'df')=df
       invisible(rval)
   } else{
-    psh <- psh %>%
-      plotly::layout(showlegend = FALSE, scene = list(camera =.plotly3d$camera))
+    psh <- psh %>% plotly::layout(showlegend = FALSE, scene=list(camera=.plotly3d$camera))
+    if(gridlines == FALSE){
+      psh <- psh %>% plotly::layout(scene = list(xaxis=.plotly3d$xaxis,
+                                                 yaxis=.plotly3d$yaxis,
+                                                 zaxis=.plotly3d$zaxis))
+    }
+
     .plotly3d$plotlyscenehandle = psh
     attr(psh, 'df') = df
     psh

R/wire3d.R

@@ -5,6 +5,8 @@
 #' @param add whether to add objects to an existing plot
 #' @param plotengine Whether to use plotting backend of 'rgl' or 'plotly'
 #' @param ... Additional arguments passed to \code{\link[rgl]{wire3d}} or 
+#' @param gridlines Whether to display gridlines when using plotly as the backend plotting
+#' engine (default: \code{FALSE})
 #' \code{\link[plotly]{add_trace} depending on the @param plotengine option choosen}
 #' @export
 #' @seealso \code{\link[rgl]{wire3d}}
@@ -25,7 +27,7 @@
 #' options(nat.plotengine = 'rgl')
 #' wire3d(kcs20.mesh,alpha = 0.1, add = FALSE, col = 'blue')
 #' }
-wire3d <- function(x, ..., add = TRUE, plotengine = getOption('nat.plotengine')) {
+wire3d <- function(x, ..., add = TRUE, gridlines = FALSE, plotengine = getOption('nat.plotengine')) {
   plotengine <- check_plotengine(plotengine)
   if (!add)
     nclear3d(plotengine = plotengine)
@@ -54,15 +56,15 @@ wire3d.default <- function(x, ...) {
 
 
 #' @export
-wire3d.plotlyshapelist3d <- function (x, override = TRUE, ...) 
+wire3d.plotlyshapelist3d <- function (x, override = TRUE, gridlines = FALSE, ...) 
 {
-  sapply(x, function(item) wire3d(item, override = override, ...))
+  sapply(x, function(item) wire3d(item, override = override, gridlines = gridlines, ...))
   psh <- openplotlyscene()$plotlyscenehandle
   psh
 }
 
 #' @export
-wire3d.plotlymesh3d <- function(x, override = TRUE, ...) {
+wire3d.plotlymesh3d <- function(x, override = TRUE, gridlines = FALSE, ...) {
 
   psh <- openplotlyscene()$plotlyscenehandle
   params=list(...)
@@ -77,6 +79,8 @@ wire3d.plotlymesh3d <- function(x, override = TRUE, ...) {
               } else 'black'
   width <- if("width" %in% names(params)) params$width else 2
 
+  label <- if("label" %in% names(params)) params$label else NULL
+
   #Gather all edges for the faces..
   #Here vb is the points of the mesh, it is the faces of the mesh (this just has the order)..
   #To get the edges, just put the put the orders(faces) and collect the points represented by them..
@@ -117,9 +121,16 @@ wire3d.plotlymesh3d <- function(x, override = TRUE, ...) {
                                    z = ptsna[,3],
                                    mode = "lines",
                                    opacity = opacity,
+                                   name = label,
                                    line = list(width = width, color = color))
 
   psh <- psh %>% plotly::layout(showlegend = FALSE, scene=list(camera=.plotly3d$camera))
+  if(gridlines == FALSE){
+    psh <- psh %>% plotly::layout(scene = list(xaxis=.plotly3d$xaxis,
+                                               yaxis=.plotly3d$yaxis,
+                                               zaxis=.plotly3d$zaxis))
+  }
+
   assign("plotlyscenehandle", psh, envir=.plotly3d)
   psh
 }

R/zzz.R

@@ -93,3 +93,10 @@ update_igraph <- FALSE
 .plotly3d$camera = list(up=list(x=0, y=0, z=1),
               center=list(x=0, y=0, z=0),
               eye=list(x=-0.1, y=-2.5, z=0.1))
+
+.plotly3d$xaxis = list(title = "", zeroline = FALSE, 
+                       showline = FALSE, showticklabels = FALSE,showgrid = FALSE)
+.plotly3d$yaxis = list(title = "", zeroline = FALSE, 
+                       showline = FALSE, showticklabels = FALSE,showgrid = FALSE)
+.plotly3d$zaxis = list(title = "", zeroline = FALSE, ticks = "",
+                        showline = FALSE, showticklabels = FALSE,showgrid = FALSE)

inst/WORDLIST

@@ -50,6 +50,7 @@ dfc
 dfs
 dir
 dirname
+DL
 dof
 doi
 donttest
@@ -64,6 +65,7 @@ dZ
 edgelist
 eg
 eigen
+elmr
 Endianness
 EndPoints
 enh
@@ -72,6 +74,7 @@ especiall
 etc
 Evers
 exe
+FAFB
 FCWB
 fftw
 fijitraces