@@ -4,6 +4,7 @@ CHANGES in VERSION 1.11.7

   as `level(value)` or `unique(value)`

 * HeatmapAnnotation: give warnings if color is defined while with no annotations

 * HeatmapAnnotation: check `col`, if it is not valid, give warnings

+* catch error when making annotation graphics

 ==========================

@@ -1306,7 +1306,7 @@ setMethod(f = "draw_heatmap_body",

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

             stop("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.")

         }

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

+        temp_image = tempfile(pattern = paste0(".heatmap_body_", object@name, "_", k, "_"), tmpdir = ".", 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 = heatmap_width*raster_quality, height = heatmap_height*raster_quality), raster_device_param))

@@ -474,7 +474,11 @@ setMethod(f = "draw",

 			for(i in seq_len(n_anno)) {

 				pushViewport(viewport(y = sum(anno_size[seq(i, n_anno)]) + sum(gap[seq(i, n_anno)]) - gap[n_anno], 

 					height = anno_size[i], just = c("center", "top")))

-				draw(object@anno_list[[i]], index, k, n)

+				oe = try(draw(object@anno_list[[i]], index, k, n))

+				if(class(oe) == "try-error") {

+					cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")

+					stop(oe)

+				}

 				upViewport()

 			}

 		} else { # put on bottom of the heatmap

@@ -482,14 +486,22 @@ setMethod(f = "draw",

 			for(i in seq_len(n_anno)) {

 				pushViewport(viewport(y = unit(1, "npc") - (sum(anno_size[seq_len(i)]) + sum(gap[seq_len(i)]) - gap[i]), 

 					height = anno_size[i], just = c("center", "bottom")))

-				draw(object@anno_list[[i]], index, k, n)

+				oe = try(draw(object@anno_list[[i]], index, k, n))

+				if(class(oe) == "try-error") {

+					cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")

+					stop(oe)

+				}

 				upViewport()

 			}

 		}

 	} else if(which == "row") {

 		for(i in seq_len(n_anno)) {

 			pushViewport(viewport(x = sum(anno_size[seq_len(i)]) + sum(gap[seq_len(i)]) - gap[i], width = anno_size[i], just = c("right", "center")))

-			draw(object@anno_list[[i]], index, k, n)

+			oe = try(draw(object@anno_list[[i]], index, k, n))

+			if(class(oe) == "try-error") {

+				cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")

+				stop(oe)

+			}

 			upViewport()

 		}

 	}

@@ -149,6 +149,39 @@ oncoPrint(mat_list,

     }, col = col)

 ```

+With a single function for `alter_fun`, you can define different graphics for different alterations.

+In following plot, you need to adjust the height of the whole plot to make sure the height for each cell

+is more than double of the width.

+

+```{r, width = 6, height = 7}

+snv_fun = function(x, y, w, h) {

+	grid.rect(x, y, w, h, gp = gpar(fill = col["snv"], col = NA))

+}

+

+indel_fun = function(x, y, r) {

+	grid.circle(x, y, r, gp = gpar(fill = col["indel"], col = NA))

+}

+

+oncoPrint(mat, get_type = function(x) strsplit(x, ";")[[1]],

+    alter_fun = function(x, y, w, h, v) {

+        n = sum(v)

+        w = convertWidth(w, "cm")*0.9

+        h = convertHeight(h, "cm")*0.9

+        l = min(unit.c(w, h))

+

+        grid.rect(x, y, w, h, gp = gpar(fill = "grey", col = NA))

+

+        if(n == 0) return(NULL)

+        if(n == 1) {

+        	if(names(which(v)) == "snv") snv_fun(x, y, l, l)

+        	if(names(which(v)) == "indel") indel_fun(x, y, l*0.5)

+        } else if(n == 2) {

+        	snv_fun(x, y-0.25*h, l, l)

+        	indel_fun(x, y+0.25*h, l*0.5)

+        }

+    }, col = col)

+```

+

 If `alter_fun` is specified as a list, the order of the elements controls the order of adding graphics. 

 There is a special element named `background` which defines how to draw background and it should be always put

 as the first element in the `alter_fun` list. In following example, backgrond color is changed to light green with borders.

@@ -173,6 +206,27 @@ oncoPrint(mat_list,

 	), col = col)

 ```

+You can customize the oncoprot by self-defining `alter_fun`. But be careful you must

+convert `w` and `h` to absolute units.

+

+```{r}

+oncoPrint(mat, get_type = function(x) strsplit(x, ";")[[1]],

+    alter_fun = list(

+        snv = function(x, y, w, h) {

+        	w = convertWidth(w, "cm")

+        	h = convertHeight(h, "cm")

+        	l = min(unit.c(w, h))

+        	grid.rect(x, y, l*0.9, l*0.9, gp = gpar(fill = col["snv"], col = NA))

+        },

+        indel = function(x, y, w, h) {

+        	w = convertWidth(w, "cm")

+        	h = convertHeight(h, "cm")

+        	r = min(unit.c(w, h))*0.5

+        	grid.circle(x, y, r*0.9, gp = gpar(fill = col["indel"], col = NA))

+        }

+    ), col = col)

+```

+

 ## Apply to cBioPortal dataset

 Now we make an oncoPrint with a real-world data. The data is retrieved from [cBioPortal](http://www.cbioportal.org/).