From 1f74e3dcae4b3bcc818bad0214fcfa2aee90595d Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Tue, 28 Apr 2026 18:16:55 +0200
Subject: [PATCH 01/12] Use faster matrix->long df conversion

---
 R/plotLabel.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/plotLabel.R b/R/plotLabel.R
index 4718a46..4cef4c5 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -59,8 +59,10 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
     if (is.numeric(i)) i <- labelNames(x)[i]
     i <- match.arg(i, labelNames(x))
     y <- label(x, i)
-    ym <- as.matrix(.get_multiscale_data(label(x, i), k))
-    df <- data.frame(x=c(col(ym)), y=c(row(ym)), z=c(ym))
+    ym <- .get_multiscale_data(label(x, i), k)
+    # Keep only indices != 0 since labels might be sparse and thus save memory by not plotting all pixels
+    idx <- BiocGenerics::which(ym != 0L, arr.ind=TRUE)
+    df <- data.frame(x=idx[,1L], y=idx[,2L], z=ym[idx])
     # transformation
     if (is.numeric(j))
       j <- CTname(y)[j]

From cb5452366d69ef0f1859760dcdf3bdda0900b22b Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Tue, 28 Apr 2026 18:17:19 +0200
Subject: [PATCH 02/12] Use system.file() directly in example

---
 R/plotLabel.R    | 3 +--
 man/plotLabel.Rd | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/R/plotLabel.R b/R/plotLabel.R
index 4cef4c5..17a5578 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -18,8 +18,7 @@
 #' @param nan character string; color for missing values (hidden by default).
 #' 
 #' @examples
-#' x <- file.path("extdata", "blobs.zarr")
-#' x <- system.file(x, package="SpatialData")
+#' x <- system.file("extdata", "blobs.zarr", package="SpatialData")
 #' x <- readSpatialData(x)
 #' 
 #' i <- "blobs_labels"
diff --git a/man/plotLabel.Rd b/man/plotLabel.Rd
index 02bc7cf..3dc738e 100644
--- a/man/plotLabel.Rd
+++ b/man/plotLabel.Rd
@@ -46,8 +46,7 @@ specifies which \code{assay} data to use (see \code{\link{valTable}}).}
 \code{SpatialData} label viz.
 }
 \examples{
-x <- file.path("extdata", "blobs.zarr")
-x <- system.file(x, package="SpatialData")
+x <- system.file("extdata", "blobs.zarr", package="SpatialData")
 x <- readSpatialData(x)
 
 i <- "blobs_labels"

From a865793201707f5ffa9a72454f3b5571dd26ca9d Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Tue, 28 Apr 2026 18:17:46 +0200
Subject: [PATCH 03/12] Avoid unnecessary setdiff()

---
 R/plotLabel.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/plotLabel.R b/R/plotLabel.R
index 17a5578..34bba4a 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -86,7 +86,7 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
         aes$fill <- aes(.data[["z"]])[[1]]
         switch(scale_type(df$z), 
             discrete={
-                val <- sort(setdiff(unique(df$z), NA))
+                val <- sort(unique(df$z), na.last=NA))
                 pal <- colorRampPalette(pal)(length(val))
                 thm <- list(
                     theme(legend.key.size=unit(0.5, "lines")),

From b0a9339259754e55a8635e4d28bbc5b295495edd Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Tue, 28 Apr 2026 18:18:11 +0200
Subject: [PATCH 04/12] Use geom_tile() to avoid warning()

---
 NAMESPACE     | 2 +-
 R/plotLabel.R | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 0520092..daf80cb 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -25,8 +25,8 @@ importFrom(ggplot2,element_line)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_blank)
 importFrom(ggplot2,geom_point)
-importFrom(ggplot2,geom_raster)
 importFrom(ggplot2,geom_sf)
+importFrom(ggplot2,geom_tile)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)
diff --git a/R/plotLabel.R b/R/plotLabel.R
index 34bba4a..b6339a1 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -50,7 +50,7 @@ NULL
 #' @importFrom methods as
 #' @importFrom ggplot2 
 #'   scale_fill_manual scale_fill_gradientn
-#'   aes geom_raster theme unit guides guide_legend
+#'   aes geom_tile theme unit guides guide_legend
 #' @importFrom SingleCellExperiment colData
 #' @export
 setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL, 
@@ -103,5 +103,5 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
             theme(legend.position="none"),
             scale_fill_manual(NULL, values=pal))
     }
-    list(thm, do.call(geom_raster, list(data=df, mapping=aes, alpha=a)))
+    list(thm, do.call(geom_tile, list(data=df, mapping=aes, alpha=a)))
 })
\ No newline at end of file

From 71c5492c7fddd1fc7cbcc51ffbcd902c8a3a3f26 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Tue, 28 Apr 2026 18:18:20 +0200
Subject: [PATCH 05/12] Avoid repeating thm<-

---
 R/plotLabel.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/plotLabel.R b/R/plotLabel.R
index b6339a1..0fc2c63 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -84,16 +84,16 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
         df$z <- getTable(x, i, c, assay=assay)[idx]
         if (c == ik) df$z <- factor(df$z)
         aes$fill <- aes(.data[["z"]])[[1]]
-        switch(scale_type(df$z), 
+        thm <- switch(scale_type(df$z), 
             discrete={
-                val <- sort(unique(df$z), na.last=NA))
+                val <- sort(unique(df$z), na.last=NA)
                 pal <- colorRampPalette(pal)(length(val))
-                thm <- list(
+                list(
                     theme(legend.key.size=unit(0.5, "lines")),
                     guides(fill=guide_legend(override.aes=list(alpha=1))),
                     scale_fill_manual(c, values=pal, breaks=val, na.value=nan))
             },
-            continuous=thm <- list(
+            continuous=list(
                 theme(legend.key.size=unit(0.5, "lines")),
                 scale_fill_gradientn(c, colors=pal, na.value=nan)))
     } else {

From cbdcbff3980c8dc6e7a683d480a4f3c7fc1f846f Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Tue, 28 Apr 2026 18:33:56 +0200
Subject: [PATCH 06/12] Reuse 'y' var

---
 R/plotLabel.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/plotLabel.R b/R/plotLabel.R
index 0fc2c63..e52e296 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -58,7 +58,7 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
     if (is.numeric(i)) i <- labelNames(x)[i]
     i <- match.arg(i, labelNames(x))
     y <- label(x, i)
-    ym <- .get_multiscale_data(label(x, i), k)
+    ym <- .get_multiscale_data(y, k)
     # Keep only indices != 0 since labels might be sparse and thus save memory by not plotting all pixels
     idx <- BiocGenerics::which(ym != 0L, arr.ind=TRUE)
     df <- data.frame(x=idx[,1L], y=idx[,2L], z=ym[idx])

From 8d9936ad719a0c1cc883454d497a296bd5f17f0f Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Tue, 28 Apr 2026 18:36:37 +0200
Subject: [PATCH 07/12] Remove unused thm var

It is immediately overwritten
---
 R/plotLabel.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/plotLabel.R b/R/plotLabel.R
index e52e296..dc285e7 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -97,7 +97,6 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
                 theme(legend.key.size=unit(0.5, "lines")),
                 scale_fill_gradientn(c, colors=pal, na.value=nan)))
     } else {
-        thm <- guides(fill="none")
         aes$fill <- aes(.data$z != 0)[[1]]
         thm <- list(
             theme(legend.position="none"),

From d2b36ccc3eefc31e8a28a326c7176d2067d47c21 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Thu, 7 May 2026 13:17:53 +0200
Subject: [PATCH 08/12] Use new workflow for transformations

---
 R/plotLabel.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/plotLabel.R b/R/plotLabel.R
index dc285e7..b9a8de5 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -58,15 +58,15 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
     if (is.numeric(i)) i <- labelNames(x)[i]
     i <- match.arg(i, labelNames(x))
     y <- label(x, i)
+    # transformation
+    if (is.numeric(j))
+      j <- CTname(y)[j]
+    y <- transform(y, j)
     ym <- .get_multiscale_data(y, k)
+  
     # Keep only indices != 0 since labels might be sparse and thus save memory by not plotting all pixels
     idx <- BiocGenerics::which(ym != 0L, arr.ind=TRUE)
     df <- data.frame(x=idx[,1L], y=idx[,2L], z=ym[idx])
-    # transformation
-    if (is.numeric(j))
-      j <- CTname(y)[j]
-    ts <- CTpath(x, i, j)
-    df[,c("x", "y")] <- .trans_xy(df[,c("x", "y")], ts)
     aes <- aes(.data[["x"]], .data[["y"]])
     if (!is.null(c)) {
         stopifnot(length(c) == 1, is.character(c))

From 28db4da1b58a1474ce69ce7e25722870ef42b8b2 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Thu, 7 May 2026 13:22:19 +0200
Subject: [PATCH 09/12] Remove now unused trans.R file

---
 R/trans.R | 39 ---------------------------------------
 1 file changed, 39 deletions(-)
 delete mode 100644 R/trans.R

diff --git a/R/trans.R b/R/trans.R
deleted file mode 100644
index 0ee4f31..0000000
--- a/R/trans.R
+++ /dev/null
@@ -1,39 +0,0 @@
-# TODO: deprecate this; all should be handled by SD
-
-# count occurrences of each coordinate space;
-# return most frequent (in order of appearance)
-.guess_space <- \(x) {
-    nms <- lapply(rownames(x), \(l) 
-        lapply(colnames(x)[[l]], \(e) 
-            CTname(x[[l]][[e]])))
-    cnt <- table(nms <- unlist(nms))
-    cnt <- cnt[unique(nms)]
-    names(which.max(cnt))
-}
-
-.trans_xy <- \(xy, ts, rev=FALSE) {
-    if (rev) ts <- rev(ts)
-    for (. in seq_along(ts)) {
-        t <- ts[[.]]$type
-        d <- ts[[.]]$data
-        d <- unlist(d)
-        if (length(d) == 3)
-            d <- d[-1]
-        switch(t, 
-            identity={},
-            scale={
-                op <- ifelse(rev, `/`, `*`)
-                xy$x <- op(xy$x, d[2])
-                xy$y <- op(xy$y, d[1])
-            },
-            rotate={
-                xy <- xy %*% .R(d*pi/180)
-            },
-            translation={
-                op <- ifelse(rev, `-`, `+`)
-                xy$x <- op(xy$x, d[2])
-                xy$y <- op(xy$y, d[1])
-            })
-    }
-    return(xy)
-}

From 4be54a70a2f8205bf4c00ed20bf3539ad2e715f1 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Thu, 7 May 2026 13:26:15 +0200
Subject: [PATCH 10/12] Flip labels

---
 R/plotLabel.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/plotLabel.R b/R/plotLabel.R
index b9a8de5..fe4601b 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -66,7 +66,8 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
   
     # Keep only indices != 0 since labels might be sparse and thus save memory by not plotting all pixels
     idx <- BiocGenerics::which(ym != 0L, arr.ind=TRUE)
-    df <- data.frame(x=idx[,1L], y=idx[,2L], z=ym[idx])
+    # All other SD elements are flipped when plotted. Let's keep the same convention here.
+    df <- data.frame(x=idx[,2L], y=idx[,1L], z=ym[idx])
     aes <- aes(.data[["x"]], .data[["y"]])
     if (!is.null(c)) {
         stopifnot(length(c) == 1, is.character(c))

From 57ff56422f4e233bb02309eade5694675f5e5028 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Thu, 7 May 2026 14:22:58 +0200
Subject: [PATCH 11/12] Fix imports

---
 DESCRIPTION   | 2 +-
 R/plotImage.R | 7 ++-----
 R/plotLabel.R | 6 +++---
 3 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b7f19f1..2e0439c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -67,8 +67,8 @@ biocViews:
     GeneExpression, 
     Transcriptomics
 License: Artistic-2.0
-RoxygenNote: 7.3.3
 Encoding: UTF-8
 VignetteBuilder: knitr
 URL: https://github.com/HelenaLC/SpatialData.plot
 BugReports: https://github.com/HelenaLC/SpatialData.plot/issues
+Config/roxygen2/version: 8.0.0
diff --git a/R/plotImage.R b/R/plotImage.R
index af979e4..3718db1 100644
--- a/R/plotImage.R
+++ b/R/plotImage.R
@@ -178,11 +178,8 @@ NULL
     list(w=df[, 1], h=df[, 2])
 }
 
-#' @importFrom ggplot2 guides geom_point 
-#'   geom_blank annotation_raster 
-#'   scale_color_identity
-#'   scale_x_continuous
-#'   scale_y_reverse
+#' @importFrom ggplot2 guides geom_point geom_blank annotation_raster 
+#' @importFrom ggplot2 scale_color_identity scale_x_continuous scale_y_reverse
 .gg_i <- \(x, w, h, pal=NULL) {
     l <- if (!is.null(names(pal))) list(
         guides(col=guide_legend(override.aes=list(alpha=1, size=2))),
diff --git a/R/plotLabel.R b/R/plotLabel.R
index fe4601b..ad56a29 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -48,9 +48,9 @@ NULL
 #' @importFrom S4Vectors metadata
 #' @importFrom rlang .data
 #' @importFrom methods as
-#' @importFrom ggplot2 
-#'   scale_fill_manual scale_fill_gradientn
-#'   aes geom_tile theme unit guides guide_legend
+#' @importFrom ggplot2 scale_fill_manual scale_fill_gradientn
+#' @importFrom ggplot2 aes theme unit guides guide_legend geom_tile
+#'   
 #' @importFrom SingleCellExperiment colData
 #' @export
 setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL, 

From bc244e71a0b9599b4a5da6b0a42a7c82da5b0b94 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Thu, 7 May 2026 14:24:01 +0200
Subject: [PATCH 12/12] Ensure labels are shifted correctly when plotted

---
 R/plotLabel.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/plotLabel.R b/R/plotLabel.R
index ad56a29..9b7b13e 100644
--- a/R/plotLabel.R
+++ b/R/plotLabel.R
@@ -63,11 +63,12 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, j=1, k=NULL, c=NULL,
       j <- CTname(y)[j]
     y <- transform(y, j)
     ym <- .get_multiscale_data(y, k)
+    wh <- .get_wh(y)
   
     # Keep only indices != 0 since labels might be sparse and thus save memory by not plotting all pixels
     idx <- BiocGenerics::which(ym != 0L, arr.ind=TRUE)
     # All other SD elements are flipped when plotted. Let's keep the same convention here.
-    df <- data.frame(x=idx[,2L], y=idx[,1L], z=ym[idx])
+    df <- data.frame(x=idx[,2L]+wh$w[1], y=idx[,1L]+wh$h[1], z=ym[idx])
     aes <- aes(.data[["x"]], .data[["y"]])
     if (!is.null(c)) {
         stopifnot(length(c) == 1, is.character(c))