Plotting slices have correct margins with partial plot

CHANGELOG.md

@@ -1,6 +1,7 @@
 ## Changes since last CRAN release
-* `7198a191 (HEAD -> master)` [_`dipterix`_]: Allow users to drag and drop value tables
-* `10ac71ad (origin/master, origin/HEAD)` [_`dipterix`_]: Allow users to hide crosshairs
+* `ef1e293d (HEAD -> master)` [_`dipterix`_]: Plotting slices have correct margins with partial plot
+* `4bd0352c (origin/master, origin/HEAD)` [_`dipterix`_]: Allow users to drag and drop value tables
+* `10ac71ad` [_`dipterix`_]: Allow users to hide crosshairs
 * `05836f94` [_`dipterix`_]: Allow `shiny` app to change current color map via proxy
 * `fbca42f4` [_`dipterix`_]: Allows drag-drop electrode color files; Added `set_electrode_data` to brain proxy class, allowing `shiny` applications to change the electrode data, set color palettes, and set value ranges in the same call
 * `a14cd3f5` [_`dipterix`_]: Allow masks to be added to `T1`; Added `D99v2` for monkey brain; Added demo code; Export `GLTF` for `datacube2`

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: threeBrain
 Type: Package
 Title: Your Advanced 3D Brain Visualization
-Version: 1.1.0.9024
+Version: 1.1.0.9025
 Authors@R: c(
     person("Zhengjia", "Wang", email = "[email protected]", role = c("aut", "cre", "cph")),
     person("John", "Magnotti", email = "[email protected]", role = c("aut", "res")),

R/class_brain.R

@@ -925,6 +925,7 @@ Brain2 <- R6::R6Class(
         graphics::points(0, 0, pch = 20, col = electrode_color,
                          cex = electrode_size)
       },
+      device_init = NULL,
       save_to = NULL, one_plot = is.null(save_to), width = 12, height = 4) {
       # DIPSAUS DEBUG START
       # self <- raveio::rave_brain('demo/DemoSubject')
@@ -1006,7 +1007,7 @@ Brain2 <- R6::R6Class(
 
       if(length(save_to) == 1 && isTRUE(is.character(save_to))) {
         if(endsWith(tolower(save_to), "png")) {
-          save_to <- sprintf("%s-%%04.png",
+          save_to <- sprintf("%s-%%04d.png",
                              gsub("[%0-9d]{0,}\\.png$", replacement = "",
                                   save_to, ignore.case = TRUE))
           grDevices::png(filename = save_to, width = width * 72,
@@ -1019,8 +1020,14 @@ Brain2 <- R6::R6Class(
                          title = "RAVE Slice Plots", bg = "black")
         }
         on.exit({ grDevices::dev.off() })
+
+      }
+      if(is.function(device_init)) {
+        device_init()
       }
 
+
+
       if( one_plot ) {
         plot_idx <- list(plot_idx)
       }

R/plot_volume-slices.R

@@ -63,6 +63,34 @@ plot_slices <- function(
     stop("`volume` must be character or threeBrain.volume")
   }
 
+  pal <- grDevices::colorRampPalette(col)(256)
+
+  more_args <- list(...)
+  more_args$axes <- FALSE
+  more_args$asp <- 1
+  more_args$col <- pal
+  more_args$zlim <- zlim
+  more_args$useRaster <- TRUE
+  more_args$main <- ''
+  more_args$xlab <- ""
+  more_args$ylab <- ""
+  default_add <- isTRUE(more_args$add)
+  # more_args$add <- FALSE
+
+  canvas_ratio <- 3
+  n_plots <- 3
+  if( default_add ) {
+    # assuming length(which) == 1 and you want to add to plot
+    canvas_ratio <- 1
+    n_plots <- 1
+  } else {
+    if(length(which) > 0) {
+      canvas_ratio <- 1
+      n_plots <- length(which)
+    }
+  }
+
+
   overlays <- lapply(seq_along(overlays), function(ii) {
     item <- overlays[[ ii ]]
     default_color <- col2hexStr(DEFAULT_COLOR_DISCRETE[[(ii - 1L) %% length(DEFAULT_COLOR_DISCRETE) + 1L]], alpha = overlay_alpha)
@@ -145,36 +173,28 @@ plot_slices <- function(
     main <- ""
   }
   main <- rep(main, ceiling(npts / length(main)))
-  pal <- grDevices::colorRampPalette(col)(256)
 
   x <- seq(-127.5, 127.5, by = abs(pixel_width * zoom)) / zoom
   nx <- length(x)
 
-  pos <- rbind(t(as.matrix(expand.grid(x, x, KEEP.OUT.ATTRS = FALSE))), 0, 1)
-
-  more_args <- list(...)
-  more_args$axes <- FALSE
-  more_args$asp <- 1
-  more_args$col <- pal
-  more_args$zlim <- zlim
-  more_args$useRaster <- TRUE
-  more_args$main <- ''
-  more_args$xlab <- ""
-  more_args$ylab <- ""
   more_args$x <- x
   more_args$y <- x
-  default_add <- isTRUE(more_args$add)
-  # more_args$add <- FALSE
+
+  pos <- rbind(t(as.matrix(expand.grid(x, x, KEEP.OUT.ATTRS = FALSE))), 0, 1)
 
   oldpar <- graphics::par(no.readonly = TRUE)
 
   if(!length(nc) || is.na(nc[[1]])) {
-    nc <- grDevices::n2mfrow(npts, asp = 1/3)[[2]]
+    nc <- grDevices::n2mfrow(npts, asp = 1/n_plots)[[2]]
   } else {
     nc <- nc[[1]]
   }
   nc <- min(max(round(nc), 1), npts)
   nr <- ceiling(npts / nc)
+
+  padding_left <- 0
+  padding_top <- 0
+
   if(!length(which)) {
     if( title_position == "left") {
       lmat <- matrix(seq_len(nr * nc), ncol = nc, byrow = FALSE)
@@ -187,6 +207,7 @@ plot_slices <- function(
         lmat,
         widths = rep(c(graphics::lcm(0.8), 1, 1, 1), times = nc)
       )
+      padding_left <- 0.8
     } else {
       lmat <- matrix(seq_len(nr * nc), ncol = nc, byrow = TRUE)
       lmat <- apply(lmat, 2, function(l) {
@@ -199,6 +220,7 @@ plot_slices <- function(
         lmat,
         heights = rep(c(graphics::lcm(0.8), 1), times = nc)
       )
+      padding_top <- 0.8
     }
 
     graphics::par(
@@ -211,10 +233,9 @@ plot_slices <- function(
     on.exit({ do.call(graphics::par, oldpar) })
   }
 
-
   # Calculate plt
   pin <- graphics::par("din")
-  pin[[1]] <- (pin[[1]] - 0.8 / 2.54) / nc / 3
+  pin[[1]] <- (pin[[1]] - padding_left / 2.54) / nc / canvas_ratio
   pin[[2]] <- pin[[2]] / nr
   if(pin[[1]] > pin[[2]]) {
     ratio <- pin[[2]] / pin[[1]]