@@ -55,8 +55,9 @@ setMethod(f = "draw_heatmap_body",

     if(!is.null(cell_fun)) {

         use_raster = FALSE

     }

-        

+   

     if(use_raster) {

+

         # write the image into a temporary file and read it back

         device_info = switch(raster_device,

             png = c("grDevices", "png", "readPNG"),

@@ -78,7 +79,19 @@ setMethod(f = "draw_heatmap_body",

         if(heatmap_width <= 0 || heatmap_height <= 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(heatmap_width < nc && heatmap_height < nr) {

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

+            matrix_is_resized = TRUE

+        } else if(heatmap_width < nc) {

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

+            matrix_is_resized = TRUE

+        } else if(heatmap_height < nr) {

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

+            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]))

@@ -86,12 +99,32 @@ setMethod(f = "draw_heatmap_body",

         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))

-        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)))

+        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")

+            }

+            col_matrix2 = map_to_colors(object@matrix_color_mapping, mat2)

+            nc2 = ncol(mat2)

+            nr2 = nrow(mat2)

+            x2 = (seq_len(nc2) - 0.5) / nc2

+            y2 = (rev(seq_len(nr2)) - 0.5) / nr2

+            expand_index2 = expand.grid(seq_len(nr2), seq_len(nc2))

+            grid.rect(x2[expand_index2[[2]]], y2[expand_index2[[1]]], width = unit(1/nc2, 'npc'), height = unit(1/nr2, 'npc'), gp = do.call('gpar', c(list(fill = col_matrix2), gp)))

+        } else {

+            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)))

+        }

         if(is.function(layer_fun)) {

-            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))

+            if(length(as.list(formals(fun))) == 7) {

+                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))

+            } 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)

+            }

         }

         dev.off2()

@@ -142,6 +175,7 @@ setMethod(f = "draw_heatmap_body",

         file.remove(temp_image)

     } else {

+

         if(any(names(gp) %in% c("type"))) {

             if(gp$type == "none") {

             } else {

@@ -161,10 +195,17 @@ setMethod(f = "draw_heatmap_body",

             }

         }

         if(is.function(layer_fun)) {

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

+            if(length(as.list(formals(fun))) == 7) {

+                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))

+            } 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))

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

+            }

         }

     }

@@ -165,6 +165,7 @@ densityHeatmap = function(data,

 		cluster_columns = cluster_columns,

 		clustering_distance_columns = clustering_distance_columns,

 		clustering_method_columns = clustering_method_columns,

+		column_dend_reorder = mean_value,

 		column_names_side = column_names_side,

 		show_column_names = show_column_names,

 		column_names_max_height = column_names_max_height,

@@ -820,3 +820,9 @@ to_unit = function(str) {

     unit(as.numeric(d), u)

 }

+

+resize_matrix = function(mat, nr, nc) {

+    w_ratio = nc/ncol(mat)

+    h_ratio = nr/nrow(mat)

+    mat[ floor(1:nr / h_ratio), floor(1:nc / w_ratio)]

+}