From 53cdffa5f6e93d2749fa91e55f90c919b3232006 Mon Sep 17 00:00:00 2001
From: bbuchsbaum <brad.buchsbaum@gmail.com>
Date: Sun, 18 May 2025 21:54:55 -0400
Subject: [PATCH] Add along parameter to plot.NeuroVol

---
 R/neurovol.R        | 12 ++++++++++--
 man/plot-methods.Rd |  2 ++
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/R/neurovol.R b/R/neurovol.R
index b8994b91..d36cea96 100644
--- a/R/neurovol.R
+++ b/R/neurovol.R
@@ -1078,6 +1078,7 @@ setMethod(f="[", signature=signature(x = "SparseNeuroVol", i = "numeric", j = "n
 #' @param x the object to display
 #' @param cmap a color map consisting of a vector of colors in hex format (e.g. \code{gray(n=255)})
 #' @param zlevels the series of slice indices to display.
+#' @param along the axis along which to slice
 #' @param irange the intensity range indicating the low and high values of the color scale.
 #' @param thresh a 2-element vector indicating the lower and upper transparency thresholds.
 #' @param alpha the level of alpha transparency
@@ -1093,10 +1094,17 @@ setMethod(f="[", signature=signature(x = "SparseNeuroVol", i = "numeric", j = "n
 #' \donttest{
 #' plot(slice)
 #' }
+#'
+#' vol_data <- array(rnorm(10 * 10 * 10), c(10, 10, 10))
+#' vol <- NeuroVol(vol_data, NeuroSpace(c(10, 10, 10)))
+#' \donttest{
+#' plot(vol, along=3)
+#' }
 setMethod("plot", signature=signature(x="NeuroVol"),
           def=function(x,
                        cmap=gray(seq(0,1,length.out=255)),
                        zlevels=unique(round(seq(1, dim(x)[3], length.out=6))),
+                       along=3,
                        irange=range(x, na.rm=TRUE),
                        thresh=c(0,0),
                        alpha=1,
@@ -1116,12 +1124,12 @@ setMethod("plot", signature=signature(x="NeuroVol"),
             # Create a data frame of all the slices specified in zlevels
             df1 <- do.call(rbind, purrr::map(zlevels, function(i) {
               if (!is.null(bgvol)) {
-                bgslice <- slice(bgvol, zlevel=i, along=3)
+                bgslice <- slice(bgvol, zlevel=i, along=along)
                 bgplane <- colorplane::IntensityColorPlane(as.numeric(bgslice), cols=bgcmap)
                 bgcols <- colorplane::map_colors(bgplane)
               }
 
-              imslice <- slice(x, zlevel=i, along=3)
+              imslice <- slice(x, zlevel=i, along=along)
               implane <- colorplane::IntensityColorPlane(as.numeric(imslice), cols=cmap, alpha=alpha)
               fgcols <- colorplane::map_colors(implane, threshold=thresh, irange=irange)
 
diff --git a/man/plot-methods.Rd b/man/plot-methods.Rd
index 421ee97a..9ea887a4 100644
--- a/man/plot-methods.Rd
+++ b/man/plot-methods.Rd
@@ -15,6 +15,7 @@
   x,
   cmap = gray(seq(0, 1, length.out = 255)),
   zlevels = unique(round(seq(1, dim(x)[3], length.out = 6))),
+  along = 3,
   irange = range(x, na.rm = TRUE),
   thresh = c(0, 0),
   alpha = 1,
@@ -30,6 +31,7 @@
 \item{irange}{the intensity range indicating the low and high values of the color scale.}
 
 \item{zlevels}{the series of slice indices to display.}
+\item{along}{the axis along which to slice}
 
 \item{thresh}{a 2-element vector indicating the lower and upper transparency thresholds.}