@@ -1,3 +1,9 @@

+CHANGES in VERSION 2.3.1

+

+* `anno_points()`: allows images as symbols.

+

+========================

+

 CHANGES in VERSION 2.1.1

 * `Heatmap()`: give error when heatmap has empty string as its name.

@@ -663,6 +663,11 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()

 			stop_wrap("`axis_direction` is not supported any more.")

 		}

 	}

+	if("pch_as_image" %in% names(other_args)) {

+		pch_as_image = other_args$pch_as_image

+	} else {

+		pch_as_image = FALSE

+	}

 	ef = function() NULL

 	if(is.null(.ENV$current_annotation_which)) {

@@ -732,8 +737,17 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()

 					default.units = "native", pch = pch[i], size = size[i])

 			}

 		} else {

-			grid.points(value[index], n - seq_along(index) + 1, gp = subset_gp(gp, index), default.units = "native", 

-				pch = pch[index], size = size[index])

+			if(pch_as_image) {

+				for(ii in seq_along(index)) {

+					pch_image = png::readPNG(pch[ index[ii] ])

+					grid.raster(pch_image, y = n - ii + 1, x = value[ index[ii] ], 

+						default.units = "native", width = size[ index[ii] ], 

+						height = size[ index[ii] ]*(nrow(pch_image)/ncol(pch_image)))

+				}

+			} else {

+				grid.points(value[index], n - seq_along(index) + 1, gp = subset_gp(gp, index), default.units = "native", 

+					pch = pch[index], size = size[index])

+			}

 		}

 		if(axis_param$side == "top") {

 			if(k > 1) axis = FALSE

@@ -756,10 +770,21 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()

 		pushViewport(viewport(yscale = data_scale, xscale = c(0.5, n+0.5)))

 		if(is.matrix(value)) {

 			for(i in seq_len(ncol(value))) {

-				grid.points(seq_along(index), value[index, i], gp = subset_gp(gp, i), default.units = "native", pch = pch[i], size = size[i])

+				grid.points(seq_along(index), value[index, i], gp = subset_gp(gp, i), 

+					default.units = "native", pch = pch[i], size = size[i])

 			}

 		} else {

-			grid.points(seq_along(index), value[index], gp = subset_gp(gp, index), default.units = "native", pch = pch[index], size = size[index])

+			if(pch_as_image) {

+				for(ii in seq_along(index)) {

+					pch_image = png::readPNG(pch[ index[ii] ])

+					grid.raster(pch_image, x = ii, value[ index[ii] ], 

+						default.units = "native", width = size[ index[ii] ], 

+						height = size[ index[ii] ]*(nrow(pch_image)/ncol(pch_image)))

+				}

+			} else {

+				grid.points(seq_along(index), value[index], gp = subset_gp(gp, index), 

+					default.units = "native", pch = pch[index], size = size[index])

+			}

 		}

 		if(axis_param$side == "left") {

 			if(k > 1) axis = FALSE

@@ -785,7 +810,7 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()

 		height = anno_size$height,

 		n = n,

 		data_scale = data_scale,

-		var_import = list(value, gp, border, pch, size, axis, axis_param, axis_grob, data_scale)

+		var_import = list(value, gp, border, pch, size, axis, axis_param, axis_grob, data_scale, pch_as_image)

 	)

 	anno@subset_rule$gp = subset_vector

@@ -87,7 +87,7 @@ make_comb_mat_from_matrix = function(x, mode, top_n_sets = Inf, min_set_size = -

 	comb_mat = t(comb_mat)

 	nc = ncol(comb_mat)

-	comb_mat2 = Matrix::Matrix(0, nrow = nrow(comb_mat), ncol = nc*(nc-1)/2, sparse = TRUE)

+	comb_mat2 = matrix(0, nrow = nrow(comb_mat), ncol = nc*(nc-1)/2)

 	rownames(comb_mat2) = rownames(comb_mat)

 	if(mode == "intersect") {

 		if(nc > 1) {

@@ -223,7 +223,7 @@ make_comb_mat_from_list = function(lt, mode, value_fun = length, top_n_sets = In

     	complement_size = value_fun(complement_set)

     }

-    comb_mat = Matrix::Matrix(FALSE, nrow = n, ncol = sum(choose(n, 1:n)), s)

+    comb_mat = matrix(FALSE, nrow = n, ncol = sum(choose(n, 1:n)))

     rownames(comb_mat) = nm

     j = 1

     for(k in 1:n) {

@@ -449,6 +449,18 @@ make_comb_mat = function(..., mode = c("distinct", "intersect", "union"),

 			value_fun = length

 		}

 	}

+

+	if(is.atomic(lt[[1]])) {

+		m = make_comb_mat_from_matrix(list_to_matrix(lt), mode = mode, top_n_sets = top_n_sets, 

+			min_set_size = min_set_size, universal_set = universal_set, complement_size = complement_size)

+		if(remove_empty_comb_set) {

+			m = m[comb_size(m) > 0]

+		}

+		if(remove_complement_set) {

+			m = m[comb_degree(m) > 0]

+		}

+		return(m)

+	}

 	m = make_comb_mat_from_list(lt, value_fun, mode = mode, top_n_sets = top_n_sets, min_set_size = min_set_size, 

 		universal_set = universal_set, complement_size = complement_size)

@@ -579,8 +591,7 @@ comb_name = function(m, readable = FALSE) {

 		nm = sapply(strsplit(nm, ""), function(x) {

 			l = as.logical(as.numeric(x))

 			paste(sn[l], collapse = "&")

-		}

-		nm = unname(nm)

+		})

 	}

 	return(nm)

@@ -129,6 +129,14 @@ draw(anno, test = "anno_points")

 anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1), which = "row")

 draw(anno, test = "anno_points")

+# pch as image

+image1 = sample(dir("/desktop-home/guz/Downloads/IcoMoon-Free-master/PNG/64px", full.names = TRUE), 10)

+x = runif(10)

+anno1 = anno_points(x, pch = image1, pch_as_image = TRUE, size = unit(5, "mm"), height = unit(4, "cm"))

+anno2 = anno_points(x, height = unit(4, "cm"))

+draw(anno1, test = "anno_points")

+draw(anno2, test = "anno_points")

+

 ##### test anno_lines ###

 anno = anno_lines(runif(10))

 draw(anno, test = "anno_lines")