fix: rework image plotting

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoVisuals
 Title: Visuals for the Giotto spatial biology analysis ecosystem
-Version: 0.1.3
+Version: 0.1.4
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre")),
@@ -82,6 +82,8 @@ Collate:
     'colorRamp2.R'
     'color_palettes.R'
     'dd.R'
+    'generics.R'
+    'gg_annotation_raster.R'
     'gg_info_layers.R'
     'globals.R'
     'gstop.R'

NEWS.md

@@ -1,7 +1,11 @@
 
-# GiottoVisuals 0.1.3 (2024/01/25)
+# GiottoVisuals 0.1.4 (2024/01/25)
 ## bug fixes
 - fix plotting color gradient when using param `point_shape = "no_border"`
+- fix image NA value [#865](https://github.com/drieslab/Giotto/issues/865) by rbutleriii
+
+## new
+- `gg_annotation_raster()` internal generic for adding a `giottoImage`, `giottoLargeImage`, or `list` thereof to a `ggplot` object
 
 # GiottoVisuals 0.1.2 (2023/01/12)
 

R/generics.R

@@ -0,0 +1,4 @@
+
+# internals
+setOldClass("gg")
+setGeneric("gg_annotation_raster", function(ggobj, gimage, ...) standardGeneric("gg_annotation_raster"))

R/gg_annotation_raster.R

@@ -0,0 +1,113 @@
+
+#' @name gg_annotation_raster
+#' @keywords internal
+#' @title Append image to ggplot as annotation_raster
+#' @param ggobj ggplot2 `gg` object
+#' @param gimage `giottoLargeImage`, `giottoImage` or `list` thereof
+#' @return `gg` object with images to plot appended as annotation rasters
+NULL
+
+#' @rdname gg_annotation_raster
+setMethod(
+  "gg_annotation_raster",
+  signature(ggobj = "gg", gimage = "list"),
+  function(ggobj, gimage, ...)
+  {
+    for(i in seq_along(gimage)) {
+      ggobj <- gg_annotation_raster(ggobj, gimage[[i]], ...)
+    }
+    return(ggobj)
+  }
+)
+
+#' @rdname gg_annotation_raster
+setMethod(
+  "gg_annotation_raster",
+  signature(ggobj = "gg", gimage = "giottoImage"),
+  function(ggobj, gimage, ...)
+  {
+    # extract min and max from object
+    my_xmax = gimage@minmax[1]
+    my_xmin = gimage@minmax[2]
+    my_ymax = gimage@minmax[3]
+    my_ymin = gimage@minmax[4]
+
+    # convert giotto image object into array
+    img_array = as.numeric(gimage@mg_object[[1]])
+
+    # extract adjustments from object
+    xmax_b = gimage@boundaries[1]
+    xmin_b = gimage@boundaries[2]
+    ymax_b = gimage@boundaries[3]
+    ymin_b = gimage@boundaries[4]
+
+    # append to ggobj
+    ggobj <- ggobj + annotation_raster(
+      img_array,
+      xmin = my_xmin-xmin_b, xmax = my_xmax+xmax_b,
+      ymin = my_ymin-ymin_b, ymax = my_ymax+ymax_b
+    )
+
+    # TODO geom_raster to accommodate single-channel
+    return(ggobj)
+  }
+)
+
+#' @rdname gg_annotation_raster
+setMethod(
+  "gg_annotation_raster",
+  signature(ggobj = "gg", gimage = "giottoLargeImage"),
+  function(ggobj, gimage, ...)
+  {
+    # get plotting minmax
+    extent = terra::ext(gimage@raster_object)[1:4]
+    xmin = extent[['xmin']]
+    xmax = extent[['xmax']]
+    ymin = extent[['ymin']]
+    ymax = extent[['ymax']]
+
+    # convert raster object into array with 3 channels
+    img_array = terra::as.array(gimage@raster_object)
+
+    # TODO: check if required, fixes NaN values
+    # replacing NA's by zero or another value directly in raster object?
+    # raster[is.na(raster[])] <- 0
+    if (is.nan(max(img_array[,,1]))) {
+      img_array[,,1][is.nan(img_array[,,1])] = max(img_array[,,1], na.rm = TRUE)
+    }
+
+    if(dim(img_array)[3] > 1) {
+      if(is.nan(max(img_array[,,2]))) {
+        img_array[,,2][is.nan(img_array[,,2])] = max(img_array[,,2], na.rm = TRUE)
+      }
+    }
+
+    if(dim(img_array)[3] > 2) {
+      if(is.nan(max(img_array[,,3]))) {
+        img_array[,,3][is.nan(img_array[,,3])] = max(img_array[,,3], na.rm = TRUE)
+      }
+    }
+
+    img_array = img_array/max(img_array, na.rm = TRUE)
+    if(dim(img_array)[3] == 1) {
+      img_array_RGB = array(NA, dim = c(dim(img_array)[1:2],3))
+      img_array_RGB[,,1:3] = img_array
+    } else {
+      img_array_RGB = img_array
+    }
+
+    # handle NA values
+    img_array_RGB[is.na(img_array_RGB)] <- 0
+
+    # append to ggobj
+    ggobj <- ggobj + annotation_raster(
+      img_array_RGB,
+      xmin = xmin, xmax = xmax,
+      ymin = ymin, ymax = ymax
+    )
+
+    # TODO geom_raster to accommodate single-channel
+    return(ggobj)
+  }
+)
+

R/gg_info_layers.R

@@ -1350,151 +1350,9 @@ plot_spat_image_layer_ggplot = function(gg_obj,
   # Assign region to plot
   gg_obj = gg_obj + geom_blank(data = spat_ext, aes_string(sdimx, sdimy))
 
-  if((inherits(gimage, 'list') | is.vector(gimage)) & length(gimage) > 1) {
-
-    for(i in 1:length(gimage)) {
-
-      if(inherits(gimage[[i]], 'giottoImage')) {
-        # extract min and max from object
-        my_xmax = gimage[[i]]@minmax[1]
-        my_xmin = gimage[[i]]@minmax[2]
-        my_ymax = gimage[[i]]@minmax[3]
-        my_ymin = gimage[[i]]@minmax[4]
-
-        # convert giotto image object into array
-        img_array = as.numeric(gimage[[i]]@mg_object[[1]])
-
-        # extract adjustments from object
-        xmax_b = gimage[[i]]@boundaries[1]
-        xmin_b = gimage[[i]]@boundaries[2]
-        ymax_b = gimage[[i]]@boundaries[3]
-        ymin_b = gimage[[i]]@boundaries[4]
-
-        gg_obj = gg_obj + annotation_raster(img_array,
-                                            xmin = my_xmin-xmin_b, xmax = my_xmax+xmax_b,
-                                            ymin = my_ymin-ymin_b, ymax = my_ymax+ymax_b)
-
-        # TODO geom_raster to accommodate single-channel
-
-      } else if(inherits(gimage[[i]], 'giottoLargeImage')) {
-        # get plotting minmax
-        extent = terra::ext(gimage[[i]]@raster_object)[1:4]
-        xmin = extent[['xmin']]
-        xmax = extent[['xmax']]
-        ymin = extent[['ymin']]
-        ymax = extent[['ymax']]
-
-        # convert raster object into array with 3 channels
-        img_array = terra::as.array(gimage[[i]]@raster_object)
-
-        # TODO: check if required, fixes NaN values
-        # replacing NA's by zero or another value directly in raster object?
-        # raster[is.na(raster[])] <- 0
-        if(is.nan(max(img_array[,,1]))) {
-          img_array[,,1][is.nan(img_array[,,1])] = max(img_array[,,1], na.rm = T)
-        }
-
-        if(dim(img_array)[3] > 1) {
-          if(is.nan(max(img_array[,,2]))) {
-            img_array[,,2][is.nan(img_array[,,2])] = max(img_array[,,2], na.rm = T)
-          }
-        }
-
-        if(dim(img_array)[3] > 2) {
-          if(is.nan(max(img_array[,,3]))) {
-            img_array[,,3][is.nan(img_array[,,3])] = max(img_array[,,3], na.rm = T)
-          }
-        }
-
-
-
+  # Assign image(s) to plot
+  gg_obj <- gg_annotation_raster(ggobj = gg_obj, gimage = gimage)
 
-        img_array = img_array/max(img_array, na.rm = TRUE)
-        if(dim(img_array)[3] == 1) {
-          img_array_RGB = array(NA, dim = c(dim(img_array)[1:2],3))
-          img_array_RGB[,,1:3] = img_array
-          img_array_RGB[is.na(img_array_RGB)] = 0
-        } else {
-          img_array_RGB = img_array
-        }
-
-        gg_obj = gg_obj + annotation_raster(img_array_RGB,
-                                            xmin = xmin, xmax = xmax,
-                                            ymin = ymin, ymax = ymax)
-
-        # TODO geom_raster to accommodate single-channel
-      }
-
-    }
-
-  } else {
-
-    if(methods::is(gimage, 'giottoImage')) {
-      # extract min and max from object
-      my_xmax = gimage@minmax[1]
-      my_xmin = gimage@minmax[2]
-      my_ymax = gimage@minmax[3]
-      my_ymin = gimage@minmax[4]
-
-      # convert giotto image object into array
-      img_array = as.numeric(gimage@mg_object[[1]])
-
-      # extract adjustments from object
-      xmax_b = gimage@boundaries[1]
-      xmin_b = gimage@boundaries[2]
-      ymax_b = gimage@boundaries[3]
-      ymin_b = gimage@boundaries[4]
-
-      gg_obj = gg_obj + annotation_raster(img_array,
-                                          xmin = my_xmin-xmin_b, xmax = my_xmax+xmax_b,
-                                          ymin = my_ymin-ymin_b, ymax = my_ymax+ymax_b)
-
-    } else if(methods::is(gimage, 'giottoLargeImage')) {
-      # get plotting minmax
-      extent = terra::ext(gimage@raster_object)[1:4]
-      xmin = extent[['xmin']]
-      xmax = extent[['xmax']]
-      ymin = extent[['ymin']]
-      ymax = extent[['ymax']]
-
-      # convert raster object into array with 3 channels
-      img_array = terra::as.array(gimage@raster_object)
-
-      # TODO: check if required, fixes NaN values
-      # replacing NA's by zero or another value directy in raster object?
-      # raster[is.na(raster[])] <- 0
-      if(is.nan(max(img_array[,,1]))) {
-        img_array[,,1][is.nan(img_array[,,1])] = max(img_array[,,1], na.rm = T)
-      }
-
-      if(dim(img_array)[3] > 1) {
-        if(is.nan(max(img_array[,,2]))) {
-          img_array[,,2][is.nan(img_array[,,2])] = max(img_array[,,2], na.rm = T)
-        }
-      }
-
-      if(dim(img_array)[3] > 2) {
-        if(is.nan(max(img_array[,,3]))) {
-          img_array[,,3][is.nan(img_array[,,3])] = max(img_array[,,3], na.rm = T)
-        }
-      }
-
-      img_array = img_array/max(img_array, na.rm = TRUE)
-      if(dim(img_array)[3] == 1) {
-        img_array_RGB = array(NA, dim = c(dim(img_array)[1:2],3))
-        img_array_RGB[,,1:3] = img_array
-        img_array_RGB[is.na(img_array_RGB)] = 0
-      } else {
-        img_array_RGB = img_array
-      }
-
-      gg_obj <- gg_obj +
-        annotation_raster(img_array_RGB,
-                          xmin = xmin, xmax = xmax,
-                          ymin = ymin, ymax = ymax)
-    }
-
-  }
 
   if(!is.null(spatlocs)) {
     gg_obj <- gg_obj +