Improvements to persp.ppp

spatstat · Oct 28, 2024 · f3cf22c · f3cf22c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: spatstat.geom
-Version: 3.3-3.004
-Date: 2024-10-24
+Version: 3.3-3.005
+Date: 2024-10-28
 Title: Geometrical Functionality of the 'spatstat' Family 
 Authors@R: c(person("Adrian", "Baddeley", 
                     role = c("aut", "cre", "cph"),
@@ -25,7 +25,7 @@ Authors@R: c(person("Adrian", "Baddeley",
 	     person("Rasmus",    "Waagepetersen", role = "ctb"))
 Maintainer: Adrian Baddeley <[email protected]>
 Depends: R (>= 3.5.0), spatstat.data (>= 3.1), spatstat.univar (>= 3.0-0), stats, graphics, grDevices, utils, methods
-Imports: spatstat.utils (>= 3.1-0), deldir (>= 1.0-2), polyclip (>= 1.10-0)
+Imports: spatstat.utils (>= 3.1-0.001), deldir (>= 1.0-2), polyclip (>= 1.10-0)
 Suggests: spatstat.random, spatstat.explore, spatstat.model, spatstat.linnet, spatial, fftwtools (>= 0.9-8), spatstat (>= 3.0)
 Description: Defines spatial data types and supports geometrical operations
 	     on them. Data types include point patterns, windows (domains),

diff --git a/NEWS b/NEWS
@@ -1,4 +1,4 @@
-        CHANGES IN spatstat.geom VERSION 3.3-3.004
+        CHANGES IN spatstat.geom VERSION 3.3-3.005
 
 OVERVIEW
 
@@ -19,9 +19,13 @@ SIGNIFICANT USER-VISIBLE CHANGES
     Now accepts arguments passed to 'as.mask' to control the pixel resolution.
 
     o persp.ppp
-    Now draws a reference scale bar for the vertical scale.
+    Now draws a reference scale bar for the vertical scale, by default.
     New arguments 'legend', 'legendpos', 'leg.args', 'leg.col'.
 
+    o persp.ppp
+    Optionally draws a symbol at the top of each spike.
+    New arguments 'type', 'point.args'.
+
         CHANGES IN spatstat.geom VERSION 3.3-3
 
 OVERVIEW

diff --git a/R/persp.ppp.R b/R/persp.ppp.R
@@ -5,21 +5,22 @@
 #'  Copyright (C) Adrian Baddeley 2024
 #'  GPL Public Licence >= 2.0
 #'
-#' $Revision: 1.4 $ $Date: 2024/10/24 03:32:24 $
+#' $Revision: 1.5 $ $Date: 2024/10/28 06:10:01 $
 
 persp.ppp <- local({
 
-  persp.ppp <- function(x, ..., main, grid=TRUE, ngrid=10,
+  persp.ppp <- function(x, ..., main, type=c("l", "b"), grid=TRUE, ngrid=10,
                         col.grid="grey", col.base="white",
                         win.args=list(),
-                        spike.args=list(),
-                        neg.args=list(), which.marks=1,
+                        spike.args=list(), 
+                        neg.args=list(), point.args=list(), which.marks=1,
                         zlab=NULL, zlim=NULL,
                         zadjust=1,
                         legend=TRUE, legendpos="bottomleft",
                         leg.args=list(lwd=4),
                         leg.col=c("black", "orange")) {
     if(missing(main)) main <- short.deparse(substitute(x))
+    type <- match.arg(type)
     W <- Window(x)
     R <- Frame(x)
     marx <- marks(x)
@@ -85,14 +86,23 @@ persp.ppp <- local({
     #' create spikes
     S <- xyzsegmentdata(x$x, x$y, 0,
                         x$x, x$y, scaled.marx)
+    #' and bubbles
+    if(type == "b")
+      P <- data.frame(x=x$x, y=x$y, z=scaled.marx)
+
     if(grid) {
       if(scaled.zlim[1] < 0) {
         #' first draw downward spikes
         downward <- (scaled.marx < 0)
         if(any(downward)) {
           SD <- S[downward, , drop=FALSE]
-          spectiveSegments(SD, neg.args, spike.args, ..., M=M)
+          spectiveSegments(SD, neg.args, spike.args, dotargs, M=M)
           S <- S[!downward, , drop=FALSE]
+          if(type == "b") {
+            PD <- P[downward, , drop=FALSE]
+            spectivePoints(PD, point.args, dotargs, M=M)
+            P <- P[!downward, , drop=FALSE]
+          }
         }
         #' plot baseline grid 
         spectiveFlatGrid(R, ngrid, M, col=col.grid)
@@ -105,6 +115,8 @@ persp.ppp <- local({
     #' draw upward spikes
     if(nrow(S) > 0) {
       spectiveSegments(S, spike.args, dotargs, M=M)
+      if(type == "b")
+        spectivePoints(P, point.args, dotargs, M=M)
     }
     #'
     if(legend) {
@@ -134,7 +146,7 @@ persp.ppp <- local({
       tixseg <- xyzsegmentdata(legxy[1], legxy[2], scaled.tix[-ntix],
                                legxy[1], legxy[2], scaled.tix[-1])
       tixcol <- rep(leg.col, ntix)[1:ntix]
-      spectiveSegments(tixseg, list(col=tixcol), leg.args, spike.args, M=M)
+      spectiveSegments(tixseg, list(col=tixcol), leg.args, M=M)
       spectiveText(legxy[1], legxy[2], scaled.tix[-c(1,ntix)],
                    labels=tix[-c(1,ntix)], pos=4, M=M)
     }
@@ -195,11 +207,21 @@ persp.ppp <- local({
     invisible(NULL)
   }
 
+  spectivePoints <- function(df, ..., M) {
+    ## arguments ... should be lists of parameters
+    p <- with(df, trans3dz(x, y, z, M))
+    do.call.matched(points.default,
+                    resolve.defaults(
+                      list(x=p$x, y=p$y),
+                      ...),
+                    extrargs=graphicsPars("points"))
+  }
+
   spectiveText <- function(x,y,z, ..., M) {
     p <- trans3dz(x, y, z, M)
     text(p$x, p$y, ...)
   }
-  
+
   persp.ppp
 })
 

diff --git a/inst/doc/packagesizes.txt b/inst/doc/packagesizes.txt
@@ -29,4 +29,4 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2024-07-05" "3.3-0" 442 1186 0 35638 15596
 "2024-07-09" "3.3-2" 442 1186 0 35638 15596
 "2024-09-18" "3.3-3" 443 1187 0 35818 15596
-"2024-10-24" "3.3-3.004" 443 1188 0 35936 15596
+"2024-10-28" "3.3-3.005" 443 1188 0 35958 15596
diff --git a/inst/info/packagesizes.txt b/inst/info/packagesizes.txt
@@ -29,4 +29,4 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2024-07-05" "3.3-0" 442 1186 0 35638 15596
 "2024-07-09" "3.3-2" 442 1186 0 35638 15596
 "2024-09-18" "3.3-3" 443 1187 0 35818 15596
-"2024-10-24" "3.3-3.004" 443 1188 0 35936 15596
+"2024-10-28" "3.3-3.005" 443 1188 0 35958 15596
diff --git a/man/persp.ppp.Rd b/man/persp.ppp.Rd
@@ -9,10 +9,14 @@
   shown as a vertical spike, with height proportional to the mark value.
 }
 \usage{
-  \method{persp}{ppp}(x, \dots, main, grid = TRUE, ngrid = 10,
+  \method{persp}{ppp}(x, \dots, main, type=c("l", "b"),
+            grid = TRUE, ngrid = 10,
             col.grid = "grey", col.base = "white",
-            win.args=list(), spike.args = list(), neg.args = list(),
-            which.marks = 1, zlab = NULL, zlim = NULL, zadjust = 1,
+            win.args=list(),
+            spike.args = list(), neg.args = list(),
+            point.args=list(), 
+            which.marks = 1,
+            zlab = NULL, zlim = NULL, zadjust = 1,
             legend=TRUE, legendpos="bottomleft",
             leg.args=list(lwd=4), leg.col=c("black", "orange"))
 }
@@ -27,11 +31,18 @@
     (for example the rotation angle \code{theta} and the elevation angle
     \code{phi})
     or passed to \code{\link[graphics]{segments}} to control the drawing
-    (for example \code{lwd} for line width).
+    of lines (for example \code{lwd} for line width)
+    or passed to \code{\link[graphics]{points.default}} to control the drawing
+    of points (for example \code{pch} for symbol type).
   }
   \item{main}{
     Optional main title for the plot.
   }
+  \item{type}{
+    Single character specifying how each observation will be plotted:
+    \code{type="l"} for lines, 
+    \code{type="b"} for both lines and points.
+  }
   \item{grid}{
     Logical value specifying whether to draw a grid of reference lines
     on the horizontal plane.
@@ -61,6 +72,10 @@
     applicable only to those spikes which have negative height
     (corresponding to a mark value which is negative).
   }
+  \item{point.args}{
+    List of arguments passed to \code{\link[graphics]{points.default}}
+    to control the drawing of the points, when \code{type="b"}.
+  }
   \item{which.marks}{
     Integer, or character name, identifying the column of marks which
     should be used, when \code{marks(x)} is a data frame.
@@ -153,6 +168,11 @@ Adrian Baddeley.
          win.args=list(col="pink", border=NA),
          spike.args=list(lwd=2), zadjust=1.5)
 
+   persp(Y, type="b",
+         theta=30, phi=20, col.base="lightblue",
+         win.args=list(col="pink", border=NA),
+         spike.args=list(lty=3), point.args=list(col="blue"), zadjust=1.5)
+
 }
 \keyword{hplot}
 \keyword{spatial}