From 8ce2cfc4306c39230e300b1d983a89e008706d30 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Sat, 23 Nov 2024 14:58:51 +0100
Subject: [PATCH 1/8] git/build ignore

---
 .Rbuildignore | 2 ++
 .gitignore    | 5 +++++
 2 files changed, 7 insertions(+)
 create mode 100644 .gitignore

diff --git a/.Rbuildignore b/.Rbuildignore
index c503c4f..d325fbf 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1 +1,3 @@
 ^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..52c1c38
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,5 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+*.Rproj
\ No newline at end of file

From b21a2139af07bb24635572eaf2044a63ed53a6c8 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Mon, 25 Nov 2024 13:52:23 +0100
Subject: [PATCH 2/8] channel support for images

---
 NAMESPACE                      |   1 +
 R/plot.R                       | 121 ++++++++++++++++++++++++++++-----
 man/plotImage.Rd               |   6 +-
 vignettes/SpatialData.plot.Rmd |  41 +++++++++++
 4 files changed, 151 insertions(+), 18 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 4871a79..dc389a3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,6 +12,7 @@ import(SpatialData)
 importFrom(DelayedArray,realize)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,int_metadata)
+importFrom(SpatialData,getZarrArrayPath)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(ggforce,geom_circle)
diff --git a/R/plot.R b/R/plot.R
index 2d19779..b5a9014 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -10,6 +10,8 @@
 #' @param k index of the scale of an image; by default (NULL), will auto-select 
 #'   scale in order to minimize memory-usage and blurring for a target size of 
 #'   800 x 800px; use Inf to plot the lowest resolution available.
+#' @param ch the image channels to be used for plotting (default: first channel)
+#' @param c plotting aesthetics; color 
 #'
 #' @return ggplot
 #'
@@ -47,6 +49,88 @@ NULL
 #' @export
 plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme 
 
+# merge image channels
+#' @noRd
+.manage_channels <- \(a, ch, c=NULL){
+  default_colors <- c("red", "green", "blue", "gray", "cyan", "magenta", "yellow")
+  if(length(ch) > length(default_colors) && is.null(c))
+    stop("You can only choose at most seven default colors!")
+  if(!is.null(c) || (is.null(c) && length(ch) > 1)) {
+    if(is.null(c))
+      c <- default_colors[1:length(ch)] 
+    c <- col2rgb(c)/255
+    a_new <- array(0, dim = c(3,dim(a)[-1]))
+    for(i in 1:dim(a)[1]){
+      a_new[1,,] <-  a_new[1,,,drop = FALSE] + a[i,,,drop = FALSE]*c[1,i]
+      a_new[2,,] <-  a_new[2,,,drop = FALSE] + a[i,,,drop = FALSE]*c[2,i]
+      a_new[3,,] <-  a_new[3,,,drop = FALSE] + a[i,,,drop = FALSE]*c[3,i]
+    }
+    a <- pmin(a_new,1)
+  } else {
+    a <- a[rep(1,3),,]
+  }
+  a
+}
+
+# check if an image is rgb or not
+#' @noRd
+.normalize_image_array <- \(a, dt){
+  # TODO: add more cases from other data types
+  if (dt == "uint8") a <- a/255
+  else if(dt == "uint16") a <- a/65535
+  else if(dt == "uint32") a <- a/4294967295
+  else if(max(a) > 1){
+    for(i in 1:dim(a)[1])
+      a[i,,] <- a[i,,]/max(a[i,,])
+  }
+  a 
+}
+
+# check if an image is rgb or not
+#' @noRd
+.is.rgb <- \(x){
+  if(!is.null(md <- x@meta))
+    labels <- md[[2]]$channels$label
+  if(length(labels) == 3)
+    if(all(labels == c("r", "g", "b")) || all(labels == seq(0,2))) {
+      return(TRUE)
+    }
+  return(FALSE)
+}
+
+# check if an image is rgb or not
+#' @importFrom SpatialData getZarrArrayPath
+#' @noRd
+.get_image_dtype <- \(a){
+  zarray_spec <- Rarr::zarr_overview(getZarrArrayPath(a), 
+                                     as_data_frame = TRUE)
+  zarray_spec$data_type
+}
+
+channelNames <- function(x){
+  if(!is.null(md <- x@meta))
+    return(md[[2]]$channels$label)
+  return(NULL)
+}
+  
+# check if channels are indices or channel names
+#' @noRd
+.ch_ind <- \(x, ch){
+  if(is.null(ch))
+    return(1)
+  lbs <- channelNames(x)
+  if(all(ch %in% lbs)){
+    return(which(lbs %in% ch))
+  } else if(!any(ch %in% lbs)){
+    message("Some channels are not found, picking first one!")
+    return(1)
+  } else {
+    message("Channels are not found, picking first one!")
+    return(1)
+  }
+  return(NULL)
+}
+
 .guess_scale <- \(x, w, h) {
     n <- length(dim(x))
     i <- ifelse(n == 3, -1, TRUE)
@@ -63,14 +147,17 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
 #' @importFrom methods as
 #' @importFrom grDevices rgb
 #' @importFrom DelayedArray realize
-.df_i <- \(x, k=NULL) {
-    a <- .get_plot_data(x, k)
-    a <- if (dim(a)[1] == 1) a[rep(1,3),,] else a
-    a <- realize(as(a, "DelayedArray"))
-    img <- rgb(
-        maxColorValue=max(a),
-        c(a[1,,]), c(a[2,,]), c(a[3,,]))
-    array(img, dim(a)[-1])
+.df_i <- \(x, k=NULL, ch=NULL, c=NULL) {
+  a <- .get_plot_data(x, k)
+  ch_i <- .ch_ind(x, ch)
+  dt <- .get_image_dtype(a)
+  if(!.is.rgb(x))
+    a <- a[ch_i,,,drop = FALSE]
+  a <- realize(as(a, "DelayedArray"))
+  a <- .normalize_image_array(a, dt)
+  if(!.is.rgb(x))
+    a <- .manage_channels(a, ch_i, c)
+  apply(a, c(2, 3), \(.) do.call(rgb, as.list(.))) 
 }
 
 .get_wh <- \(x, i, j) {
@@ -91,13 +178,13 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
 
 #' @rdname plotImage
 #' @export
-setMethod("plotImage", "SpatialData", \(x, i=1, j=1, k=NULL) {
-    if (is.numeric(i)) 
-        i <- imageNames(x)[i]
-    y <- image(x, i)
-    if (is.numeric(j)) 
-        j <- CTname(y)[j]
-    df <- .df_i(y, k)
-    wh <- .get_wh(x, i, j)
-    .gg_i(df, wh$w, wh$h)
+setMethod("plotImage", "SpatialData", \(x, i=1, j=1, k=NULL, ch=NULL, c=NULL) {
+  if (is.numeric(i)) 
+    i <- imageNames(x)[i]
+  y <- image(x, i)
+  if (is.numeric(j)) 
+    j <- CTname(y)[j]
+  df <- .df_i(y, k, ch, c)
+  wh <- .get_wh(x, i, j)
+  .gg_i(df, wh$w, wh$h)
 })
\ No newline at end of file
diff --git a/man/plotImage.Rd b/man/plotImage.Rd
index ae8a64e..93ae0f6 100644
--- a/man/plotImage.Rd
+++ b/man/plotImage.Rd
@@ -8,7 +8,7 @@
 \usage{
 plotSpatialData()
 
-\S4method{plotImage}{SpatialData}(x, i = 1, j = 1, k = NULL)
+\S4method{plotImage}{SpatialData}(x, i = 1, j = 1, k = NULL, ch = NULL, c = NULL)
 }
 \arguments{
 \item{x}{\code{\link{SpatialData}} object.}
@@ -20,6 +20,10 @@ plotSpatialData()
 \item{k}{index of the scale of an image; by default (NULL), will auto-select 
 scale in order to minimize memory-usage and blurring for a target size of 
 800 x 800px; use Inf to plot the lowest resolution available.}
+
+\item{ch}{the image channels to be used for plotting (default: first channel)}
+
+\item{c}{plotting aesthetics; color}
 }
 \value{
 ggplot
diff --git a/vignettes/SpatialData.plot.Rmd b/vignettes/SpatialData.plot.Rmd
index 63c3d38..2d7debe 100644
--- a/vignettes/SpatialData.plot.Rmd
+++ b/vignettes/SpatialData.plot.Rmd
@@ -231,6 +231,47 @@ wrap_plots(nrow=1, lapply(seq(3), \(.)
     plot_layout(guides="collect")
 ```
 
+## CyCIF (MCMICRO)
+
+Small lung adenocarcinoma, 250 MB; 1 image, 2 labels, 2 tables.
+
+```{r mcmicro-read}
+dir.create(td <- tempfile())
+pa <- unzip_spd_demo(
+    zipname="mcmicro_io.zip", 
+    dest=td, source="biocOSN")
+(x <- readSpatialData(pa))
+```
+Getting channel names for the image
+
+```{r mcmicro-channels}
+channelNames(image(x,1))
+```
+
+Plotting with multiple image channels.
+
+```{r mcmicro-plot}
+plotSpatialData() + plotImage(x, 1, ch = c("DNA_6", "ELANE", "CD57"), c = c("blue", "cyan", "yellow"))
+```
+
+## IMC (Steinbock)
+
+4 different cancers (SCCHN, BCC, NSCLC, CRC), 820 MB; 14 images, 14 labels, 1 table.
+
+```{r steinbock-read}
+dir.create(td <- tempfile())
+pa <- unzip_spd_demo(
+    zipname="steinbock_io.zip", 
+    dest=td, source="biocOSN")
+(x <- readSpatialData(pa))
+```
+
+Plotting with multiple image channels.
+
+```{r steinbock-plot}
+plotSpatialData() + plotImage(x, 1, ch = c(0,1,2), c = c("blue", "cyan", "yellow"))
+```
+
 # Session info
 
 ```{r sessionInfo, echo=FALSE}

From 315aebcf4cfbc1fb8f9c143d98fc68065d3cb2d0 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Mon, 25 Nov 2024 13:55:58 +0100
Subject: [PATCH 3/8] update vignette

---
 vignettes/SpatialData.plot.Rmd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/vignettes/SpatialData.plot.Rmd b/vignettes/SpatialData.plot.Rmd
index 690a192..f99ffde 100644
--- a/vignettes/SpatialData.plot.Rmd
+++ b/vignettes/SpatialData.plot.Rmd
@@ -249,6 +249,7 @@ pa <- unzip_spd_demo(
     dest=td, source="biocOSN")
 (x <- readSpatialData(pa))
 ```
+
 Getting channel names for the image
 
 ```{r mcmicro-channels}

From 87086c10ef96cf3c498d2170037321ba4c6ef7a2 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Mon, 25 Nov 2024 14:18:26 +0100
Subject: [PATCH 4/8] define default colors and data type max values

---
 R/plotImage.R                  | 31 ++++++++++++++-----------------
 R/utils.R                      | 13 ++++++++++++-
 vignettes/SpatialData.plot.Rmd |  1 +
 3 files changed, 27 insertions(+), 18 deletions(-)

diff --git a/R/plotImage.R b/R/plotImage.R
index 6c964ab..eb8c4e7 100644
--- a/R/plotImage.R
+++ b/R/plotImage.R
@@ -36,8 +36,7 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
 # merge image channels
 #' @noRd
 .manage_channels <- \(a, ch, c=NULL){
-  default_colors <- c("red", "green", "blue", "gray", "cyan", "magenta", "yellow")
-  if(length(ch) > length(default_colors) && is.null(c))
+  if(length(ch) > length(.DEFAULT_COLORS) && is.null(c))
     stop("You can only choose at most seven default colors!")
   if(!is.null(c) || (is.null(c) && length(ch) > 1)) {
     if(is.null(c))
@@ -56,13 +55,20 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
   a
 }
 
+# check if an image is rgb or not
+#' @importFrom SpatialData getZarrArrayPath
+#' @noRd
+.get_image_dtype <- \(a){
+  zarray_spec <- Rarr::zarr_overview(getZarrArrayPath(a), 
+                                     as_data_frame = TRUE)
+  zarray_spec$data_type
+}
+
 # check if an image is rgb or not
 #' @noRd
 .normalize_image_array <- \(a, dt){
-  # TODO: add more cases from other data types
-  if (dt == "uint8") a <- a/255
-  else if(dt == "uint16") a <- a/65535
-  else if(dt == "uint32") a <- a/4294967295
+  dt <- .get_image_dtype(a)
+  if(dt %in% names(.DTYPE_MAX_VALUES)) a <- a/.DTYPE_MAX_VALUES[[dt]]
   else if(max(a) > 1){
     for(i in 1:dim(a)[1])
       a[i,,] <- a[i,,]/max(a[i,,])
@@ -71,26 +77,18 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
 }
 
 # check if an image is rgb or not
+# NOTE: some rgb channels are named as 0:2
 #' @noRd
 .is.rgb <- \(x){
   if(!is.null(md <- x@meta))
     labels <- md[[2]]$channels$label
   if(length(labels) == 3)
-    if(all(labels == c("r", "g", "b")) || all(labels == seq(0,2))) {
+    if(all(labels %in% c("r", "g", "b")) || all(labels %in% seq(0,2))) {
       return(TRUE)
     }
   return(FALSE)
 }
 
-# check if an image is rgb or not
-#' @importFrom SpatialData getZarrArrayPath
-#' @noRd
-.get_image_dtype <- \(a){
-  zarray_spec <- Rarr::zarr_overview(getZarrArrayPath(a), 
-                                     as_data_frame = TRUE)
-  zarray_spec$data_type
-}
-
 channelNames <- function(x){
   if(!is.null(md <- x@meta))
     return(md[[2]]$channels$label)
@@ -134,7 +132,6 @@ channelNames <- function(x){
 .df_i <- \(x, k=NULL, ch=NULL, c=NULL) {
   a <- .get_plot_data(x, k)
   ch_i <- .ch_ind(x, ch)
-  dt <- .get_image_dtype(a)
   if(!.is.rgb(x))
     a <- a[ch_i,,,drop = FALSE]
   a <- realize(as(a, "DelayedArray"))
diff --git a/R/utils.R b/R/utils.R
index efdbfef..6eca93e 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -33,4 +33,15 @@
         plot.title=element_text(hjust=0.5),
         axis.text=element_text(color="grey"),
         axis.ticks=element_line(color="grey"))
-)
\ No newline at end of file
+)
+
+# default colors (from ImageJ/Fiji)
+.DEFAULT_COLORS <- c("red", "green", "blue", "gray", "cyan", "magenta", "yellow")
+
+# image data type factors (max values)
+# TODO: add more cases from other data types
+# https://doc.embedded-wizard.de/uint-type
+.DTYPE_MAX_VALUES <- list("uint8" = 255,
+                          "uint16" = 65535,
+                          "uint32" = 4294967295,
+                          "uint64" = 2^64 - 1)
\ No newline at end of file
diff --git a/vignettes/SpatialData.plot.Rmd b/vignettes/SpatialData.plot.Rmd
index f99ffde..d755882 100644
--- a/vignettes/SpatialData.plot.Rmd
+++ b/vignettes/SpatialData.plot.Rmd
@@ -278,6 +278,7 @@ Plotting with multiple image channels.
 
 ```{r steinbock-plot}
 plotSpatialData() + plotImage(x, 1, ch = c(0,1,2), c = c("blue", "cyan", "yellow"))
+# plotSpatialData() + plotImage(x, 1, ch = c(0,1,2), c = c("blue", "cyan", "yellow"))
 ```
 
 # Masking

From a07f88cd0e8e095362b7c38d5a4b62d25bdd8991 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Mon, 25 Nov 2024 14:51:36 +0100
Subject: [PATCH 5/8] define some tests and correct behaviour

---
 R/plotImage.R                   | 21 +++++++++++++--------
 tests/testthat/test-plotImage.R | 22 ++++++++++++++++++++++
 2 files changed, 35 insertions(+), 8 deletions(-)
 create mode 100644 tests/testthat/test-plotImage.R

diff --git a/R/plotImage.R b/R/plotImage.R
index eb8c4e7..6ae239f 100644
--- a/R/plotImage.R
+++ b/R/plotImage.R
@@ -33,7 +33,8 @@ NULL
 #' @export
 plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme 
 
-# merge image channels
+# merge/manage image channels
+# if no colors and channels defined, return the first channel
 #' @noRd
 .manage_channels <- \(a, ch, c=NULL){
   if(length(ch) > length(.DEFAULT_COLORS) && is.null(c))
@@ -61,13 +62,14 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
 .get_image_dtype <- \(a){
   zarray_spec <- Rarr::zarr_overview(getZarrArrayPath(a), 
                                      as_data_frame = TRUE)
-  zarray_spec$data_type
+  if("data_type" %in% names(zarray_spec))
+    return(zarray_spec$data_type)
+  return(NULL)
 }
 
-# check if an image is rgb or not
+# normalize the image data given its data type
 #' @noRd
 .normalize_image_array <- \(a, dt){
-  dt <- .get_image_dtype(a)
   if(dt %in% names(.DTYPE_MAX_VALUES)) a <- a/.DTYPE_MAX_VALUES[[dt]]
   else if(max(a) > 1){
     for(i in 1:dim(a)[1])
@@ -89,8 +91,10 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
   return(FALSE)
 }
 
+#' get channel names
+#' @export
 channelNames <- function(x){
-  if(!is.null(md <- x@meta))
+  if(!is.null(md <- attr(x, "meta")))
     return(md[[2]]$channels$label)
   return(NULL)
 }
@@ -102,12 +106,12 @@ channelNames <- function(x){
     return(1)
   lbs <- channelNames(x)
   if(all(ch %in% lbs)){
-    return(which(lbs %in% ch))
+    return(match(ch,lbs))
   } else if(!any(ch %in% lbs)){
-    message("Some channels are not found, picking first one!")
+    warning("Some channels are not found, picking first one!")
     return(1)
   } else {
-    message("Channels are not found, picking first one!")
+    warning("Channels are not found, picking first one!")
     return(1)
   }
   return(NULL)
@@ -134,6 +138,7 @@ channelNames <- function(x){
   ch_i <- .ch_ind(x, ch)
   if(!.is.rgb(x))
     a <- a[ch_i,,,drop = FALSE]
+  dt <- .get_image_dtype(a)
   a <- realize(as(a, "DelayedArray"))
   a <- .normalize_image_array(a, dt)
   if(!.is.rgb(x))
diff --git a/tests/testthat/test-plotImage.R b/tests/testthat/test-plotImage.R
new file mode 100644
index 0000000..aa8e473
--- /dev/null
+++ b/tests/testthat/test-plotImage.R
@@ -0,0 +1,22 @@
+require(SpatialData, quietly=TRUE)
+x <- file.path("extdata", "blobs.zarr")
+x <- system.file(x, package="SpatialData")
+x <- readSpatialData(x, tables=FALSE)
+
+test_that("get/check channel names", {
+  
+  # get channel names
+  expect_equal(channelNames(image(x,1)), c(0,1,2))
+
+  # get indices of channels
+  expect_equal(.ch_ind(image(x,1), ch = c(2,0,1)), c(3,1,2))
+  expect_warning(expect_equal(.ch_ind(image(x,1), ch = 45), 1)) # return first if no matching channel
+  
+  # .is.rgb
+  expect_true(.is.rgb(image(x,1)))
+})
+
+# TODO: any tests for image array normalization ? 
+test_that(".normalize_image_array", {
+  skip()
+})

From 3638fb88f24f92bb2aded0fed9ae9f39d4104339 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Mon, 25 Nov 2024 15:32:29 +0100
Subject: [PATCH 6/8] check, test and run examples

---
 DESCRIPTION                    |   3 ++-
 NAMESPACE                      |   1 +
 R/plotImage.R                  |   5 ++---
 tests/testthat/Rplots.pdf      | Bin 0 -> 4271 bytes
 vignettes/SpatialData.plot.Rmd |   4 ++--
 5 files changed, 7 insertions(+), 6 deletions(-)
 create mode 100644 tests/testthat/Rplots.pdf

diff --git a/DESCRIPTION b/DESCRIPTION
index 5960769..e35dbac 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -41,7 +41,8 @@ Imports:
     rlang,
     sf,
     S4Vectors,
-    SingleCellExperiment
+    SingleCellExperiment,
+    Rarr
 Suggests:
     BiocStyle,
     ggnewscale,
diff --git a/NAMESPACE b/NAMESPACE
index 4275200..e5188d0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,6 +10,7 @@ exportMethods(scale)
 exportMethods(translation)
 import(SpatialData)
 importFrom(DelayedArray,realize)
+importFrom(Rarr,zarr_overview)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,int_colData)
 importFrom(SingleCellExperiment,int_metadata)
diff --git a/R/plotImage.R b/R/plotImage.R
index 6ae239f..2f7bd3d 100644
--- a/R/plotImage.R
+++ b/R/plotImage.R
@@ -41,7 +41,7 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
     stop("You can only choose at most seven default colors!")
   if(!is.null(c) || (is.null(c) && length(ch) > 1)) {
     if(is.null(c))
-      c <- default_colors[1:length(ch)] 
+      c <- .DEFAULT_COLORS[1:length(ch)] 
     c <- col2rgb(c)/255
     a_new <- array(0, dim = c(3,dim(a)[-1]))
     for(i in 1:dim(a)[1]){
@@ -58,6 +58,7 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
 
 # check if an image is rgb or not
 #' @importFrom SpatialData getZarrArrayPath
+#' @importFrom Rarr zarr_overview
 #' @noRd
 .get_image_dtype <- \(a){
   zarray_spec <- Rarr::zarr_overview(getZarrArrayPath(a), 
@@ -91,8 +92,6 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
   return(FALSE)
 }
 
-#' get channel names
-#' @export
 channelNames <- function(x){
   if(!is.null(md <- attr(x, "meta")))
     return(md[[2]]$channels$label)
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..27de6dc7904a6e5959c03d13a86d357c7e73e2a1
GIT binary patch
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diff --git a/vignettes/SpatialData.plot.Rmd b/vignettes/SpatialData.plot.Rmd
index d755882..d41bf9b 100644
--- a/vignettes/SpatialData.plot.Rmd
+++ b/vignettes/SpatialData.plot.Rmd
@@ -253,7 +253,8 @@ pa <- unzip_spd_demo(
 Getting channel names for the image
 
 ```{r mcmicro-channels}
-channelNames(image(x,1))
+# TODO: add this to SpatialData as an ImageArray method
+# channelNames(image(x,1))
 ```
 
 Plotting with multiple image channels.
@@ -278,7 +279,6 @@ Plotting with multiple image channels.
 
 ```{r steinbock-plot}
 plotSpatialData() + plotImage(x, 1, ch = c(0,1,2), c = c("blue", "cyan", "yellow"))
-# plotSpatialData() + plotImage(x, 1, ch = c(0,1,2), c = c("blue", "cyan", "yellow"))
 ```
 
 # Masking

From 8601647d48cdeee96f940f522b2b9f7939ac452d Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Mon, 25 Nov 2024 15:38:14 +0100
Subject: [PATCH 7/8] remove redundant files

---
 tests/testthat/Rplots.pdf | Bin 4271 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 tests/testthat/Rplots.pdf

diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
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index 27de6dc7904a6e5959c03d13a86d357c7e73e2a1..0000000000000000000000000000000000000000
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From c8d3640af3c9a4e2568f2f4bc33d973b8fd68f5f Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Mon, 25 Nov 2024 16:16:17 +0100
Subject: [PATCH 8/8] add anndataR=FALSE

---
 vignettes/SpatialData.plot.Rmd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/vignettes/SpatialData.plot.Rmd b/vignettes/SpatialData.plot.Rmd
index d41bf9b..bff6cce 100644
--- a/vignettes/SpatialData.plot.Rmd
+++ b/vignettes/SpatialData.plot.Rmd
@@ -247,7 +247,7 @@ dir.create(td <- tempfile())
 pa <- unzip_spd_demo(
     zipname="mcmicro_io.zip", 
     dest=td, source="biocOSN")
-(x <- readSpatialData(pa))
+(x <- readSpatialData(pa, anndataR=FALSE))
 ```
 
 Getting channel names for the image
@@ -272,7 +272,7 @@ dir.create(td <- tempfile())
 pa <- unzip_spd_demo(
     zipname="steinbock_io.zip", 
     dest=td, source="biocOSN")
-(x <- readSpatialData(pa))
+(x <- readSpatialData(pa, anndataR=FALSE))
 ```
 
 Plotting with multiple image channels.