@@ -228,7 +228,7 @@ setMethod(f = "draw_heatmap_body",

             }

             attr(image, "width") = heatmap_width_pt

             attr(image, "height") = heatmap_height_pt

-            assign(".image", image, envir = .GlobalEnv)

+            # assign(".image", image, envir = .GlobalEnv)

         }

         ########################

@@ -60,6 +60,9 @@ setMethod(f = "draw_heatmap_body",

     if(!is.null(cell_fun)) {

         use_raster = FALSE

     }

+    if(identical(object@matrix_param$gp$type, "none")) {

+        use_raster = FALSE

+    }

     if(use_raster) {

@@ -139,8 +139,22 @@ setMethod(f = "draw_heatmap_body",

             temp_image_width = ceiling(max(heatmap_width_pt, 1))

             temp_image_height = ceiling(max(heatmap_height_pt, 1))

         }

-        do.call(device_fun, c(list(filename = temp_image, 

-            width = temp_image_width, height = temp_image_height), raster_device_param))

+        temp_image_width = as.integer(temp_image_width)

+        temp_image_height = as.integer(temp_image_height)

+

+        if(!is.na(ht_opt$raster_temp_image_max_width)) {

+            temp_image_width = min(temp_image_width, ht_opt$raster_temp_image_max_width)

+        }

+        if(!is.na(ht_opt$raster_temp_image_max_height)) {

+            temp_image_height = min(temp_image_height, ht_opt$raster_temp_image_max_height)

+        }

+

+        oe = try(do.call(device_fun, c(list(filename = temp_image, 

+            width = temp_image_width, height = temp_image_height), raster_device_param)))

+        if(inherits(oe, "try-error")) {

+            stop_wrap(qq("The size of the temporary image for rasterization is too huge (@{temp_image_width} x @{temp_image_height} px) that it is cannot be handled by the device function `@{device_info[1]}:@{raster_device}()`. Please reduce the maximal size of temporary image by setting proper values for `ht_opt$raster_temp_image_max_width` and `ht_opt$raster_temp_image_max_height`."))

+        }

+

         if(object@heatmap_param$verbose) {

             qqcat("saving into a temp image (.@{device_info[2]}) with size @{temp_image_width}x@{temp_image_height}px.\n")

         }

@@ -363,6 +363,7 @@ setMethod(f = "draw_dend",

     if(is.null(max_height)) {

         max_height = dend_heights(dend)

     }

+    if(max_height == 0) max_height = 1

     if(side %in% c("left", "right")) {

         xscale = c(0, max_height)

@@ -92,6 +92,10 @@ setMethod(f = "draw_heatmap_body",

         heatmap_width_pt = max(1, ceiling(convertWidth(unit(1, "npc"), "bigpts", valueOnly = TRUE)))

         heatmap_height_pt = max(1, ceiling(convertHeight(unit(1, "npc"), "bigpts", valueOnly = TRUE)))

+        if(raster_quality < 1) raster_quality = 1

+        heatmap_width_pt = ceiling(heatmap_width_pt * raster_quality)

+        heatmap_height_pt = ceiling(heatmap_height_pt * raster_quality)

+

         matrix_is_resized = FALSE

         # resize on the matrix

         raster_resize_mat = object@heatmap_param$raster_resize_mat

@@ -132,14 +136,8 @@ setMethod(f = "draw_heatmap_body",

             temp_image_width = ceiling(max(heatmap_width_pt, 1))

             temp_image_height = ceiling(max(heatmap_height_pt, 1))

         } else {

-            if(is.character(raster_quality)) {

-                temp_image_width = ceiling(max(heatmap_width_pt, nc, 1))

-                temp_image_height = ceiling(max(heatmap_height_pt, nr, 1))

-            } else {

-                if(raster_quality < 1) raster_quality = 1

-                temp_image_width = ceiling(max(heatmap_width_pt*raster_quality, 1))

-                temp_image_height = ceiling(max(heatmap_height_pt*raster_quality, 1))

-            }

+            temp_image_width = ceiling(max(heatmap_width_pt, 1))

+            temp_image_height = ceiling(max(heatmap_height_pt, 1))

         }

         do.call(device_fun, c(list(filename = temp_image, 

             width = temp_image_width, height = temp_image_height), raster_device_param))

@@ -44,7 +44,10 @@ setMethod(f = "draw_heatmap_body",

     pushViewport(viewport(name = paste(object@name, "heatmap_body", kr, kc, sep = "_"), ...))

     mat = object@matrix[row_order, column_order, drop = FALSE]

-    col_matrix = map_to_colors(object@matrix_color_mapping, mat)

+    oe = try(col_matrix <- map_to_colors(object@matrix_color_mapping, mat), silent = TRUE)

+    if(inherits(oe, "try-error")) {

+        col_matrix = matrix(NA, nrow = nrow(mat), ncol = ncol(mat))

+    }

     nc = ncol(mat)

     nr = nrow(mat)

@@ -613,7 +613,11 @@ setMethod(f = "draw_annotation",

                 anno_mark_param$.pos = .pos

                 anno_mark_param$index = unlist(ro_lt)

-                anno_mark_param$vp_height = convertHeight(unit(1, "npc"), "cm")

+                if(abs(par("din")[2] - grDevices::dev.size("in")[2]) < 1e-6) {

+                    anno_mark_param$vp_height = convertHeight(unit(1, "npc"), "cm")  

+                } else {

+                    anno_mark_param$vp_height = convertHeight(unit(1, "npc"), "cm")*(par("din")[2]/grDevices::dev.size("in")[2])*0.9742

+                }

                 anno_mark_param$vp_width = unit(1, "npc")

                 anno_mark_param$vp_just = "top"

                 anno_mark_param$vp_x = unit(0.5, "npc")

@@ -644,7 +648,11 @@ setMethod(f = "draw_annotation",

                 anno_mark_param$index = unlist(co_lt)

                 anno_mark_param$vp_height = unit(1, "npc")

-                anno_mark_param$vp_width = convertWidth(unit(1, "npc"), "cm")

+                if(abs(par("din")[1] - grDevices::dev.size("in")[1]) < 1e-6) {

+                    anno_mark_param$vp_width = convertWidth(unit(1, "npc"), "cm")

+                } else {

+                    anno_mark_param$vp_width = convertWidth(unit(1, "npc"), "cm")*(par("din")[1]/grDevices::dev.size("in")[1])*0.945

+                }

                 anno_mark_param$vp_just = "left"

                 anno_mark_param$vp_x = unit(0, "npc")

                 anno_mark_param$vp_y = unit(0.5, "npc")

@@ -505,6 +505,14 @@ setMethod(f = "draw_title",

         "row" = object@row_title_param$just,

         "column" = object@column_title_param$just)

+    if(!is.null(ht_opt$TITLE_PADDING)) {

+        title_padding = ht_opt$TITLE_PADDING

+    } else {

+        title_padding = unit(c(0, 0), "points")

+        title_padding[1] = title_padding[1] + unit(5.5, "points") + 

+            convertHeight(grobDescent(textGrob(label = "jA", gp = gp)), "inches")

+    }

+

     if(which == "row") {

         pushViewport(viewport(name = paste(object@name, "row_title", k, sep = "_"), clip = FALSE, ...))

@@ -512,9 +520,9 @@ setMethod(f = "draw_title",

         if("border" %in% names(gp2)) gp2$col = gp2$border

         if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)

         if(side == "left") {

-            grid.text(title, x = unit(1, "npc") - ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

+            grid.text(title, x = unit(1, "npc") - title_padding[1], rot = rot, just = just, gp = gp)

         } else {

-            grid.text(title, x = ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

+            grid.text(title, x = title_padding[1], rot = rot, just = just, gp = gp)

         }

         upViewport()

     } else {

@@ -523,9 +531,9 @@ setMethod(f = "draw_title",

         if("border" %in% names(gp2)) gp2$col = gp2$border

         if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)

         if(side == "top") {

-            grid.text(title, y = ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

+            grid.text(title, y = title_padding[1], rot = rot, just = just, gp = gp)

         } else {

-            grid.text(title, y = unit(1, "npc") - ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

+            grid.text(title, y = unit(1, "npc") - title_padding[1], rot = rot, just = just, gp = gp)

         }

         upViewport()

     }

@@ -77,6 +77,14 @@ setMethod(f = "draw_heatmap_body",

             stop_wrap(paste0("Need ", device_info[2], " package to read image."))

         }

+        if(raster_device %in% c("png", "jpeg", "tiff")) {

+            if(! "type" %in% names(raster_device_param)) {

+                if(capabilities("cairo")) {

+                    raster_device_param$type = "cairo"

+                }

+            }

+        }

+

         # can we get the size of the heatmap body?

         heatmap_width_pt = max(1, ceiling(convertWidth(unit(1, "npc"), "bigpts", valueOnly = TRUE)))

         heatmap_height_pt = max(1, ceiling(convertHeight(unit(1, "npc"), "bigpts", valueOnly = TRUE)))

@@ -188,7 +196,7 @@ setMethod(f = "draw_heatmap_body",

         grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"), interpolate = FALSE)

-        ### only for testing ###

+        ### only for testing the temp image size ###

         if(ht_opt("__export_image_size__")) {

             if(inherits(image, "magick-image")) {

                 image = as.raster(image)

@@ -504,7 +504,7 @@ setMethod(f = "draw_title",

         if("border" %in% names(gp2)) gp2$col = gp2$border

         if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)

         if(side == "left") {

-            grid.text(title, x = unit(1, "npc") - ht_opt$TITLE_PADDING[2], rot = rot, just = just, gp = gp)

+            grid.text(title, x = unit(1, "npc") - ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

         } else {

             grid.text(title, x = ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

         }

@@ -517,7 +517,7 @@ setMethod(f = "draw_title",

         if(side == "top") {

             grid.text(title, y = ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

         } else {

-            grid.text(title, y = unit(1, "npc") - ht_opt$TITLE_PADDING[2], rot = rot, just = just, gp = gp)

+            grid.text(title, y = unit(1, "npc") - ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

         }

         upViewport()

     }

@@ -152,12 +152,12 @@ setMethod(f = "draw_heatmap_body",

         if(is.function(layer_fun)) {

             if(length(as.list(formals(layer_fun))) == 7) {

                 layer_fun(column_order[ expand_index[[2]] ], row_order[ expand_index[[1]] ], 

-                    x[expand_index[[2]]], y[expand_index[[1]]],

+                    unit(x[expand_index[[2]]], "npc"), unit(y[expand_index[[1]]], "npc"),

                     unit(rep(1/nc, nrow(expand_index)), "npc"), unit(rep(1/nr, nrow(expand_index)), "npc"),

                     as.vector(col_matrix))

             } else {

                 layer_fun(column_order[ expand_index[[2]] ], row_order[ expand_index[[1]] ], 

-                    x[expand_index[[2]]], y[expand_index[[1]]],

+                    unit(x[expand_index[[2]]], "npc"), unit(y[expand_index[[1]]], "npc"),

                     unit(rep(1/nc, nrow(expand_index)), "npc"), unit(rep(1/nr, nrow(expand_index)), "npc"),

                     as.vector(col_matrix), kr, kc)

             }

@@ -231,14 +231,14 @@ setMethod(f = "draw_heatmap_body",

         if(is.function(layer_fun)) {

             if(length(as.list(formals(layer_fun))) == 7) {

                 layer_fun(column_order[ expand_index[[2]] ], row_order[ expand_index[[1]] ], 

-                    x[expand_index[[2]]], y[expand_index[[1]]],

+                    unit(x[expand_index[[2]]], "npc"), unit(y[expand_index[[1]]], "npc"),

                     unit(rep(1/nc, nrow(expand_index)), "npc"), unit(rep(1/nr, nrow(expand_index)), "npc"),

                     as.vector(col_matrix))

             } else {

                 layer_fun(column_order[ expand_index[[2]] ], row_order[ expand_index[[1]] ], 

-                x[expand_index[[2]]], y[expand_index[[1]]],

-                unit(rep(1/nc, nrow(expand_index)), "npc"), unit(rep(1/nr, nrow(expand_index)), "npc"),

-                as.vector(col_matrix), kr, kc)

+                    unit(x[expand_index[[2]]], "npc"), unit(y[expand_index[[1]]], "npc"),

+                    unit(rep(1/nc, nrow(expand_index)), "npc"), unit(rep(1/nr, nrow(expand_index)), "npc"),

+                    as.vector(col_matrix), kr, kc)

             }

         }

     }

@@ -111,7 +111,7 @@ setMethod(f = "draw_heatmap_body",

         }

         temp_dir = tempdir()

-        temp_image = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", kr, "_", kc), tmpdir = temp_dir, fileext = paste0(".", device_info[2]))

+        temp_image = tempfile(pattern = paste0(".heatmap_body_", digest::digest(object@name), "_", kr, "_", kc), tmpdir = temp_dir, fileext = paste0(".", device_info[2]))

         device_fun = getFromNamespace(raster_device, ns = device_info[1])

         if(raster_by_magick) {

@@ -176,6 +176,7 @@ setMethod(f = "draw_heatmap_body",

             }

             image = magick::image_read(temp_image)

             image = magick::image_resize(image, paste0(heatmap_width_pt, "x", heatmap_height_pt, "!"), filter = raster_magick_filter)

+            image = as.raster(image)

         } else {

             if(object@heatmap_param$verbose) {

                 qqcat("image is read by @{device_info[2]}::@{device_info[3]}\n")

@@ -183,7 +184,7 @@ setMethod(f = "draw_heatmap_body",

             image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)

         }

         # validate image, there might be white horizontal lines and vertical lines 

-        image = validate_raster_matrix(image, mat, object@matrix_color_mapping)

+        # image = validate_raster_matrix(image, mat, object@matrix_color_mapping)

         grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"), interpolate = FALSE)

@@ -262,11 +263,29 @@ setMethod(f = "draw_heatmap_body",

 # careful: row orders of rgb and mat are reversed

 # rgb: values change from 0 to 1

 validate_raster_matrix = function(rgb, mat, col_mapping) {

-    # if(any(rgb[, 1, 1] == 1 & rgb[, 1, 2] == 1 & rgb[, 1, 3] == 1)) {

-    #     if(nrow(rgb) < nrow(mat)) {

+    if(is.character(rgb)) {

+        dim = dim(rgb)

+        x = col2rgb(rgb)/255

+        rgb = array(dim = c(dim, 3))

+        rgb[, , 1] = matrix(x[1, ], nrow = dim[1], ncol = dim[2], byrow = TRUE)

+        rgb[, , 2] = matrix(x[2, ], nrow = dim[1], ncol = dim[2], byrow = TRUE)

+        rgb[, , 3] = matrix(x[3, ], nrow = dim[1], ncol = dim[2], byrow = TRUE)

+    }

+    # check rows

+    white_row = NULL

+    white_column = NULL

+    if(any( abs(rgb[, 1, 1] - 1) < 1e-10 & abs(rgb[, 1, 2] - 1) < 1e-10 & abs(rgb[, 1, 3] - 1)< 1e-10 )) {

+        white_row = which( abs(rowMeans(rgb[, , 1]) - 1) < 1e-10 & 

+                           abs(rowMeans(rgb[, , 2]) - 1) < 1e-10 & 

+                           abs(rowMeans(rgb[, , 3]) - 1) < 1e-10 )

+    }

+    if(any( abs(rgb[1, , 1] - 1) < 1e-10 & abs(rgb[1, , 2] - 1) < 1e-10 & abs(rgb[1, , 3] - 1)< 1e-10 )) {

+        white_column = which( abs(colMeans(rgb[, , 1]) - 1) < 0.1 & 

+                              abs(colMeans(rgb[, , 2]) - 1) < 0.1 & 

+                              abs(colMeans(rgb[, , 3]) - 1) < 0.1 )

+    }

-    #     }

-    # }

+    # estimate while rows and columns

     rgb

 }

@@ -262,11 +262,11 @@ setMethod(f = "draw_heatmap_body",

 # careful: row orders of rgb and mat are reversed

 # rgb: values change from 0 to 1

 validate_raster_matrix = function(rgb, mat, col_mapping) {

-    if(any(rgb[, 1, 1] == 1 & rgb[, 1, 2] == 1 & rgb[, 1, 3] == 1)) {

-        if(nrow(rgb) < nrow(mat)) {

+    # if(any(rgb[, 1, 1] == 1 & rgb[, 1, 2] == 1 & rgb[, 1, 3] == 1)) {

+    #     if(nrow(rgb) < nrow(mat)) {

-        }

-    }

+    #     }

+    # }

     rgb

 }

@@ -176,14 +176,16 @@ setMethod(f = "draw_heatmap_body",

             }

             image = magick::image_read(temp_image)

             image = magick::image_resize(image, paste0(heatmap_width_pt, "x", heatmap_height_pt, "!"), filter = raster_magick_filter)

-            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"), interpolate = FALSE)

         } else {

             if(object@heatmap_param$verbose) {

                 qqcat("image is read by @{device_info[2]}::@{device_info[3]}\n")

             }

             image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)

-            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"), interpolate = FALSE)

         }

+        # validate image, there might be white horizontal lines and vertical lines 

+        image = validate_raster_matrix(image, mat, object@matrix_color_mapping)

+

+        grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"), interpolate = FALSE)

         ### only for testing ###

         if(ht_opt("__export_image_size__")) {

@@ -256,6 +258,18 @@ setMethod(f = "draw_heatmap_body",

 })

+# check white lines in the RGB matrix, and re-fill the color from mat with color_mapping

+# careful: row orders of rgb and mat are reversed

+# rgb: values change from 0 to 1

+validate_raster_matrix = function(rgb, mat, col_mapping) {

+    if(any(rgb[, 1, 1] == 1 & rgb[, 1, 2] == 1 & rgb[, 1, 3] == 1)) {

+        if(nrow(rgb) < nrow(mat)) {

+

+        }

+    }

+    rgb

+}

+

 is_windows = function() {

     tolower(.Platform$OS.type) == "windows"

 }

@@ -67,7 +67,8 @@ setMethod(f = "draw_heatmap_body",

             tiff = c("grDevices", "tiff", "readTIFF"),

             CairoPNG = c("Cairo", "png", "readPNG"),

             CairoJPEG = c("Cairo", "jpeg", "readJPEG"),

-            CairoTIFF = c("Cairo", "tiff", "readTIFF")

+            CairoTIFF = c("Cairo", "tiff", "readTIFF"),

+            agg_png = c("ragg", "png", "readPNG")

         )

         if(!requireNamespace(device_info[1])) {

             stop_wrap(paste0("Need ", device_info[1], " package to write image."))

@@ -470,9 +470,9 @@ setMethod(f = "draw_title",

         if("border" %in% names(gp2)) gp2$col = gp2$border

         if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)

         if(side == "left") {

-            grid.text(title, x = unit(1, "npc") - ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

+            grid.text(title, x = unit(1, "npc") - ht_opt$TITLE_PADDING[2], rot = rot, just = just, gp = gp)

         } else {

-            grid.text(title, x = ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

+            grid.text(title, x = ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

         }

         upViewport()

     } else {

@@ -481,9 +481,9 @@ setMethod(f = "draw_title",

         if("border" %in% names(gp2)) gp2$col = gp2$border

         if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)

         if(side == "top") {

-            grid.text(title, y = ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

+            grid.text(title, y = ht_opt$TITLE_PADDING[1], rot = rot, just = just, gp = gp)

         } else {

-            grid.text(title, y = unit(1, "npc") - ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

+            grid.text(title, y = unit(1, "npc") - ht_opt$TITLE_PADDING[2], rot = rot, just = just, gp = gp)

         }

         upViewport()

     }

@@ -77,11 +77,8 @@ setMethod(f = "draw_heatmap_body",

         }

         # can we get the size of the heatmap body?

-        heatmap_width_pt = ceiling(convertWidth(unit(1, "npc"), "bigpts", valueOnly = TRUE))

-        heatmap_height_pt = ceiling(convertHeight(unit(1, "npc"), "bigpts", valueOnly = TRUE))

-        if(heatmap_width_pt <= 0 || heatmap_height_pt <= 0) {

-            stop_wrap("The width or height of the raster image is zero, maybe you forget to turn off the previous graphic device or it was corrupted. Run `dev.off()` to close it.")

-        }

+        heatmap_width_pt = max(1, ceiling(convertWidth(unit(1, "npc"), "bigpts", valueOnly = TRUE)))

+        heatmap_height_pt = max(1, ceiling(convertHeight(unit(1, "npc"), "bigpts", valueOnly = TRUE)))

         matrix_is_resized = FALSE

         # resize on the matrix

@@ -127,6 +127,7 @@ setMethod(f = "draw_heatmap_body",

                 temp_image_width = ceiling(max(heatmap_width_pt, nc, 1))

                 temp_image_height = ceiling(max(heatmap_height_pt, nr, 1))

             } else {

+                if(raster_quality < 1) raster_quality = 1

                 temp_image_width = ceiling(max(heatmap_width_pt*raster_quality, 1))

                 temp_image_height = ceiling(max(heatmap_height_pt*raster_quality, 1))

             }

@@ -173,7 +174,7 @@ setMethod(f = "draw_heatmap_body",

                 qqcat("image is read by magick.\n")

             }

             if(!requireNamespace("magick")) {

-                stop_wrap("magick package should be installed.")

+                stop_wrap("'magick' package should be installed.")

             }

             image = magick::image_read(temp_image)

             image = magick::image_resize(image, paste0(heatmap_width_pt, "x", heatmap_height_pt, "!"), filter = raster_magick_filter)

@@ -108,12 +108,29 @@ setMethod(f = "draw_heatmap_body",

             }

         }

+        if(matrix_is_resized) {

+            raster_by_magick = FALSE

+        }

+

         temp_dir = tempdir()

         temp_image = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", kr, "_", kc), tmpdir = temp_dir, fileext = paste0(".", device_info[2]))

         device_fun = getFromNamespace(raster_device, ns = device_info[1])

-        temp_image_width = ceiling(max(heatmap_width_pt, nc, 1))

-        temp_image_height = ceiling(max(heatmap_height_pt, nr, 1))

+        if(raster_by_magick) {

+            temp_image_width = ceiling(max(heatmap_width_pt, nc, 1))

+            temp_image_height = ceiling(max(heatmap_height_pt, nr, 1))

+        } else if(matrix_is_resized) {

+            temp_image_width = ceiling(max(heatmap_width_pt, 1))

+            temp_image_height = ceiling(max(heatmap_height_pt, 1))

+        } else {

+            if(is.character(raster_quality)) {

+                temp_image_width = ceiling(max(heatmap_width_pt, nc, 1))

+                temp_image_height = ceiling(max(heatmap_height_pt, nr, 1))

+            } else {

+                temp_image_width = ceiling(max(heatmap_width_pt*raster_quality, 1))

+                temp_image_height = ceiling(max(heatmap_height_pt*raster_quality, 1))

+            }

+        }

         do.call(device_fun, c(list(filename = temp_image, 

             width = temp_image_width, height = temp_image_height), raster_device_param))

         if(object@heatmap_param$verbose) {

@@ -160,13 +177,13 @@ setMethod(f = "draw_heatmap_body",

             }

             image = magick::image_read(temp_image)

             image = magick::image_resize(image, paste0(heatmap_width_pt, "x", heatmap_height_pt, "!"), filter = raster_magick_filter)

-            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

+            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"), interpolate = FALSE)

         } else {

             if(object@heatmap_param$verbose) {

                 qqcat("image is read by @{device_info[2]}::@{device_info[3]}\n")

             }

             image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)

-            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

+            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"), interpolate = FALSE)

         }

         ### only for testing ###

@@ -224,8 +224,14 @@ setMethod(f = "draw_heatmap_body",

         }

     }

-    if(!identical(border, FALSE) && !identical(border, NA)) {

+    if(!(identical(border, FALSE) || identical(border, NA))) {

         border_gp = object@matrix_param$border_gp

+        if(!identical(border, TRUE)) {

+            border_gp$col = border

+        }

+        if("fill" %in% names(border_gp)) {

+            message_wrap("`fill` is ignored in `border_gp`. The value for `fill` is always 'transparent'.")

+        }

         border_gp$fill = "transparent"

         grid.rect(gp = border_gp)

     }

@@ -170,19 +170,21 @@ setMethod(f = "draw_heatmap_body",

         }

         ### only for testing ###

-        if(inherits(image, "magick-image")) {

-            image = as.raster(image)

-        } else {

-            tf = tempfile()

-            png(tf, width = heatmap_width_pt, height = heatmap_height_pt)

-            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

-            dev.off()

-            image = as.raster(png::readPNG(tf))

-            file.remove(tf)   

+        if(ht_opt("__export_image_size__")) {

+            if(inherits(image, "magick-image")) {

+                image = as.raster(image)

+            } else {

+                tf = tempfile()

+                png(tf, width = heatmap_width_pt, height = heatmap_height_pt)

+                grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

+                dev.off()

+                image = as.raster(png::readPNG(tf))

+                file.remove(tf)   

+            }

+            attr(image, "width") = heatmap_width_pt

+            attr(image, "height") = heatmap_height_pt

+            assign(".image", image, envir = .GlobalEnv)

         }

-        attr(image, "width") = heatmap_width_pt

-        attr(image, "height") = heatmap_height_pt

-        .GlobalEnv$image = image

         ########################

         file.remove(temp_image)

@@ -75,6 +75,7 @@ setMethod(f = "draw_heatmap_body",

         if(!requireNamespace(device_info[2])) {

             stop_wrap(paste0("Need ", device_info[2], " package to read image."))

         }

+

         # can we get the size of the heatmap body?

         heatmap_width_pt = ceiling(convertWidth(unit(1, "npc"), "bigpts", valueOnly = TRUE))

         heatmap_height_pt = ceiling(convertHeight(unit(1, "npc"), "bigpts", valueOnly = TRUE))

@@ -167,6 +168,23 @@ setMethod(f = "draw_heatmap_body",

             image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)

             grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

         }

+

+        ### only for testing ###

+        if(inherits(image, "magick-image")) {

+            image = as.raster(image)

+        } else {

+            tf = tempfile()

+            png(tf, width = heatmap_width_pt, height = heatmap_height_pt)

+            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

+            dev.off()

+            image = as.raster(png::readPNG(tf))

+            file.remove(tf)   

+        }

+        attr(image, "width") = heatmap_width_pt

+        attr(image, "height") = heatmap_height_pt

+        .GlobalEnv$image = image

+        ########################

+

         file.remove(temp_image)

     } else {

@@ -37,6 +37,8 @@ setMethod(f = "draw_heatmap_body",

     raster_device = object@heatmap_param$raster_device

     raster_quality = object@heatmap_param$raster_quality

     raster_device_param = object@heatmap_param$raster_device_param

+    raster_by_magick = object@heatmap_param$raster_by_magick

+    raster_magick_filter = object@heatmap_param$raster_magick_filter

     if(length(raster_device_param) == 0) raster_device_param = list()

     pushViewport(viewport(name = paste(object@name, "heatmap_body", kr, kc, sep = "_"), ...))

@@ -74,36 +76,51 @@ setMethod(f = "draw_heatmap_body",

             stop_wrap(paste0("Need ", device_info[2], " package to read image."))

         }

         # can we get the size of the heatmap body?

-        heatmap_width = convertWidth(unit(1, "npc"), "bigpts", valueOnly = TRUE)

-        heatmap_height = convertHeight(unit(1, "npc"), "bigpts", valueOnly = TRUE)

-        if(heatmap_width <= 0 || heatmap_height <= 0) {

+        heatmap_width_pt = ceiling(convertWidth(unit(1, "npc"), "bigpts", valueOnly = TRUE))

+        heatmap_height_pt = ceiling(convertHeight(unit(1, "npc"), "bigpts", valueOnly = TRUE))

+        if(heatmap_width_pt <= 0 || heatmap_height_pt <= 0) {

             stop_wrap("The width or height of the raster image is zero, maybe you forget to turn off the previous graphic device or it was corrupted. Run `dev.off()` to close it.")

         }

         matrix_is_resized = FALSE

-        if(object@heatmap_param$raster_resize) {

-            if(heatmap_width < nc && heatmap_height < nr) {

-                mat2 = resize_matrix(mat, nr = heatmap_height, nc = heatmap_width)

+        # resize on the matrix

+        raster_resize_mat = object@heatmap_param$raster_resize_mat

+        if(!identical(raster_resize_mat, FALSE)) {

+            if(is.logical(raster_resize_mat)) {

+                raster_resize_mat_fun = function(x) mean(x, na.rm = TRUE)

+            } else {

+                if(!inherits(raster_resize_mat, "function")) {

+                    stop_wrap("`raster_resize_mat` should be set as logical scalar or a function.")

+                }

+                raster_resize_mat_fun = raster_resize_mat

+            }

+

+            if(heatmap_width_pt < nc && heatmap_height_pt < nr) {

+                mat2 = resize_matrix(mat, nr = heatmap_height_pt, nc = heatmap_width_pt, fun = raster_resize_mat_fun)

                 matrix_is_resized = TRUE

-            } else if(heatmap_width < nc) {

-                mat2 = resize_matrix(mat, nr = nr, nc = heatmap_width)

+            } else if(heatmap_width_pt < nc) {

+                mat2 = resize_matrix(mat, nr = nr, nc = heatmap_width_pt, fun = raster_resize_mat_fun)

                 matrix_is_resized = TRUE

-            } else if(heatmap_height < nr) {

-                mat2 = resize_matrix(mat, nr = heatmap_height, nc = nc)

+            } else if(heatmap_height_pt < nr) {

+                mat2 = resize_matrix(mat, nr = heatmap_height_pt, nc = nc, fun = raster_resize_mat_fun)

                 matrix_is_resized = TRUE

             }

         }

         temp_dir = tempdir()

-                # dir.create(tmp_dir, showWarnings = FALSE)

         temp_image = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", kr, "_", kc), tmpdir = temp_dir, fileext = paste0(".", device_info[2]))

-        #getFromNamespace(raster_device, ns = device_info[1])(temp_image, width = heatmap_width*raster_quality, height = heatmap_height*raster_quality)

         device_fun = getFromNamespace(raster_device, ns = device_info[1])

-        do.call(device_fun, c(list(filename = temp_image, width = max(c(heatmap_width*raster_quality, 1)), height = max(c(heatmap_height*raster_quality, 1))), raster_device_param))

+        temp_image_width = ceiling(max(heatmap_width_pt, nc, 1))

+        temp_image_height = ceiling(max(heatmap_height_pt, nr, 1))

+        do.call(device_fun, c(list(filename = temp_image, 

+            width = temp_image_width, height = temp_image_height), raster_device_param))

+        if(object@heatmap_param$verbose) {

+            qqcat("saving into a temp image (.@{device_info[2]}) with size @{temp_image_width}x@{temp_image_height}px.\n")

+        }

         if(matrix_is_resized) {

             if(object@heatmap_param$verbose) {

-                qqcat("resize the matrix from (@{nrow(mat)} x @{ncol(mat)}) to (@{nrow(mat2)} x @{ncol(mat2)}).\n")

+                qqcat("resize the matrix from (@{nrow(mat)}x@{ncol(mat)}) to (@{nrow(mat2)}x@{ncol(mat2)}).\n")

             }

             col_matrix2 = map_to_colors(object@matrix_color_mapping, mat2)

             nc2 = ncol(mat2)

@@ -129,51 +146,27 @@ setMethod(f = "draw_heatmap_body",

             }

         }

         dev.off2()

-        

-        # ############################################

-        # ## make the heatmap body in a another process

-        # temp_R_data = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", kr, "_", kc), tmpdir = temp_dir, fileext = paste0(".RData"))

-        # temp_R_file = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", kr, "_", kc), tmpdir = temp_dir, fileext = paste0(".R"))

-        # if(Sys.info()["sysname"] == "Windows") {

-        #     temp_image = gsub("\\\\", "/", temp_image)

-        #     temp_R_data = gsub("\\\\", "/", temp_R_data)

-        #     temp_R_file = gsub("\\\\", "/", temp_R_file)

-        # }

-        # save(device_fun, device_info, temp_image, heatmap_width, raster_quality, heatmap_height, raster_device_param,

-        #     gp, x, expand_index, nc, nr, col_matrix, row_order, column_order, y,

-        #     file = temp_R_data)

-        # R_cmd = qq("

-        # library(@{device_info[1]})

-        # library(grid)

-        # load('@{temp_R_data}')

-        # do.call('device_fun', c(list(filename = temp_image, width = max(c(heatmap_width*raster_quality, 1)), height = max(c(heatmap_height*raster_quality, 1))), raster_device_param))

-        # grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, 'npc'), height = unit(1/nr, 'npc'), gp = do.call('gpar', c(list(fill = col_matrix), gp)))

-        # dev.off()

-        # q(save = 'no')

-        # ", code.pattern = "@\\{CODE\\}")

-        # writeLines(R_cmd, con = temp_R_file)

-        # if(grepl(" ", temp_R_file)) {

-        #     if(is_windows()) {

-        #         oe = try(system(qq("\"@{normalizePath(R_binary(), winslash='/')}\" --vanilla < \'@{temp_R_file}\'", code.pattern = "@\\{CODE\\}"), ignore.stdout = TRUE, ignore.stderr = TRUE, show.output.on.console = FALSE), silent = TRUE)

-        #     } else {

-        #         oe = try(system(qq("\"@{normalizePath(R_binary(), winslash='/')}\" --vanilla < \'@{temp_R_file}\'", code.pattern = "@\\{CODE\\}"), ignore.stdout = TRUE, ignore.stderr = TRUE), silent = TRUE)

-        #     }

-        # } else {

-        #     if(is_windows()) {

-        #         oe = try(system(qq("\"@{normalizePath(R_binary(), winslash='/')}\" --vanilla < @{temp_R_file}", code.pattern = "@\\{CODE\\}"), ignore.stdout = TRUE, ignore.stderr = TRUE, show.output.on.console = FALSE), silent = TRUE)

-        #     } else {

-        #         oe = try(system(qq("\"@{normalizePath(R_binary(), winslash='/')}\" --vanilla < @{temp_R_file}", code.pattern = "@\\{CODE\\}"), ignore.stdout = TRUE, ignore.stderr = TRUE), silent = TRUE)

-        #     }

-        # }

-        # ############################################

-        # file.remove(temp_R_data)

-        # file.remove(temp_R_file)

-        # if(inherits(oe, "try-error")) {

-        #     stop(oe)

-        # }

-        image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)

-        image = as.raster(image)

-        grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

+

+        if(object@heatmap_param$verbose) {

+            qqcat("resize the temp image to a size @{heatmap_width_pt}x@{heatmap_height_pt}px.\n")

+        }

+        if(raster_by_magick) {

+            if(object@heatmap_param$verbose) {

+                qqcat("image is read by magick.\n")

+            }

+            if(!requireNamespace("magick")) {

+                stop_wrap("magick package should be installed.")

+            }

+            image = magick::image_read(temp_image)

+            image = magick::image_resize(image, paste0(heatmap_width_pt, "x", heatmap_height_pt, "!"), filter = raster_magick_filter)

+            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

+        } else {

+            if(object@heatmap_param$verbose) {

+                qqcat("image is read by @{device_info[2]}::@{device_info[3]}\n")

+            }

+            image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)

+            grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))

+        }

         file.remove(temp_image)

     } else {

@@ -211,8 +211,9 @@ setMethod(f = "draw_heatmap_body",

         }

     }

-    if(!identical(border, FALSE)) {

+    if(!identical(border, FALSE) && !identical(border, NA)) {

         border_gp = object@matrix_param$border_gp

+        border_gp$fill = "transparent"

         grid.rect(gp = border_gp)

     }

@@ -212,7 +212,8 @@ setMethod(f = "draw_heatmap_body",

     }

     if(!identical(border, FALSE)) {

-        grid.rect(gp = gpar(fill = "transparent", col = border))

+        border_gp = object@matrix_param$border_gp

+        grid.rect(gp = border_gp)

     }

     upViewport()

@@ -430,9 +430,9 @@ setMethod(f = "draw_title",

     if(which == "row") {

         pushViewport(viewport(name = paste(object@name, "row_title", k, sep = "_"), clip = FALSE, ...))

-        if("fill" %in% names(gp)) {

-            grid.rect(gp = gpar(fill = gp$fill))

-        }

+        gp2 = gp

+        if("border" %in% names(gp2)) gp2$col = gp2$border

+        if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)

         if(side == "left") {

             grid.text(title, x = unit(1, "npc") - ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

         } else {

@@ -441,9 +441,9 @@ setMethod(f = "draw_title",

         upViewport()

     } else {

         pushViewport(viewport(name = paste(object@name, "column_title", k, sep = "_"), clip = FALSE, ...))

-        if("fill" %in% names(gp)) {

-            grid.rect(gp = gpar(fill = gp$fill))

-        }

+        gp2 = gp

+        if("border" %in% names(gp2)) gp2$col = gp2$border

+        if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)

         if(side == "top") {

             grid.text(title, y = ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

         } else {

@@ -509,7 +509,7 @@ setMethod(f = "draw_annotation",

         if(n_slice > 1) {

             all_anno_type = anno_type(annotation)

-            if("anno_mark" %in% all_anno_type) {

+            if(any(c("anno_zoom", "anno_mark") %in% all_anno_type)) {

                 ## only make the anno_mark annotation

                 ro_lt = object@row_order_list

                 # calcualte the position of each row with taking "gaps" into account

@@ -541,7 +541,7 @@ setMethod(f = "draw_annotation",

         if(n_slice > 1) {

             all_anno_type = anno_type(annotation)

-            if("anno_mark" %in% all_anno_type) {

+            if(any(c("anno_zoom", "anno_mark") %in% all_anno_type)) {

                 ## only make the anno_mark annotation

                 co_lt = object@column_order_list

                 .scale = c(0, 1)

@@ -500,7 +500,73 @@ setMethod(f = "draw_annotation",

         n = length(object@row_order_list)

     }

+    ## deal with the special anno_mark

+    anno_mark_param = list()

+    if(which %in% c("left", "right")) {

+        slice_y = object@layout$slice$y

+        n_slice = length(slice_y)

+        slice_height = object@layout$slice$height

+

+        if(n_slice > 1) {

+            all_anno_type = anno_type(annotation)

+            if("anno_mark" %in% all_anno_type) {

+                ## only make the anno_mark annotation

+                ro_lt = object@row_order_list

+                # calcualte the position of each row with taking "gaps" into account

+                .scale = c(0, 1)

+

+                .pos = NULL

+                for(i in seq_along(ro_lt)) {

+                    # assume slices are align to top `slice_just` contains "top"

+                    .pos1 = slice_y[i] - (seq_along(ro_lt[[i]]) - 0.5)/length(ro_lt[[i]]) * slice_height[i]

+                    .pos1 = convertY(.pos1, "native", valueOnly = TRUE)

+                    .pos = c(.pos, .pos1)

+                }

+

+                anno_mark_param$.scale = .scale

+                anno_mark_param$.pos = .pos

+                anno_mark_param$index = unlist(ro_lt)

+                

+                anno_mark_param$vp_height = convertHeight(unit(1, "npc"), "cm")

+                anno_mark_param$vp_width = unit(1, "npc")

+                anno_mark_param$vp_just = "top"

+                anno_mark_param$vp_x = unit(0.5, "npc")

+                anno_mark_param$vp_y = unit(1, "npc")

+            }

+        }

+    } else {

+        slice_x = object@layout$slice$x

+        n_slice = length(slice_x)

+        slice_width = object@layout$slice$width

+

+        if(n_slice > 1) {

+            all_anno_type = anno_type(annotation)

+            if("anno_mark" %in% all_anno_type) {

+                ## only make the anno_mark annotation

+                co_lt = object@column_order_list

+                .scale = c(0, 1)

+

+                .pos = NULL

+                for(i in seq_along(co_lt)) {

+                    .pos1 = slice_x[i] + (seq_along(co_lt[[i]]) - 0.5)/length(co_lt[[i]]) * slice_width[i]

+                    .pos1 = convertX(.pos1, "native", valueOnly = TRUE)

+                    .pos = c(.pos, .pos1)

+                }

+

+                anno_mark_param$.scale = .scale

+                anno_mark_param$.pos = .pos

+                anno_mark_param$index = unlist(co_lt)

+                

+                anno_mark_param$vp_height = unit(1, "npc")

+                anno_mark_param$vp_width = convertWidth(unit(1, "npc"), "cm")

+                anno_mark_param$vp_just = "left"

+                anno_mark_param$vp_x = unit(0, "npc")

+                anno_mark_param$vp_y = unit(0.5, "npc")

+            }

+        }

+    }

+

     pushViewport(viewport(...))