@@ -2,7 +2,7 @@ Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

 Version: 1.99.5

-Date: 2019-01-31

+Date: 2019-02-12

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

@@ -3,6 +3,9 @@ CHANGES in VERSION 1.99.5

 * add `UpSet()` and some related functions to make Upset plots

 * fixed bugs of drawing legends

 * add `test_alter_fun()`

+* `HeatmapAnnotation()`: fixed a bug for setting `height` when all annotations are simple annotations.

+* `default_col()`: if the fraction of positive values in the matrix is in (0.3, 0.7), the color mapping

+  is symmetric to zero.

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

@@ -1041,7 +1041,7 @@ setMethod(f = "re_size",

 	height = NULL, 

 	width = NULL, 

 	anno_simple_size = ht_opt$anno_simple_size,

-	simple_anno_size_adjust = FALSE) {

+	simple_anno_size_adjust = NULL) {

 	if(object@which == "column") {

 		if(!missing(width) || !missing(annotation_width)) {

@@ -1054,9 +1054,17 @@ setMethod(f = "re_size",

 		}

 	}

+	all_simple_annotation = all(sapply(object@anno_list, function(x) is_simple_annotation(x) || is_matrix_annotation(x)))

+	if(is.null(simple_anno_size_adjust)) {

+		if(all_simple_annotation) {

+			simple_anno_size_adjust = TRUE

+		} else {

+			simple_anno_size_adjust = FALSE

+		}

+	}

 	which = object@which

 	if(!simple_anno_size_adjust) {

-		if(all(sapply(object@anno_list, function(x) is_simple_annotation(x) || is_matrix_annotation(x)))) {

+		if(all_simple_annotation) {

 			if(which == "column") {

 				height = sum(object@anno_size) + sum(object@gap) - object@gap[length(object@gap)]

 				object@height = convertHeight(height, "mm")

@@ -1064,6 +1072,9 @@ setMethod(f = "re_size",

 				width = sum(object@anno_size) + sum(object@gap) - object@gap[length(object@gap)]

 				object@width = convertWidth(width, "mm")

 			}

+			if(ht_opt$verbose) {

+				message_wrap("`simple_anno_size_adjust` is set to FALSE and all annotations are simple annotations or matrix annotations, the heights of all annotations are not adjusted.")

+			}

 			return(object)

 		}

 	}

@@ -1083,6 +1094,11 @@ setMethod(f = "re_size",

 		if(is.null(annotation_height)) {

 			is_annotation_size_set = FALSE

 		} else {

+			if(length(annotation_height) == 1) {

+				if(!inherits(annotation_height, "unit")) {

+					annotation_height = rep(annotation_height, length(object@anno_list))

+				}

+			}

 			if(length(annotation_height) == 1) {

 				if(length(object@anno_list) > 1) {

 					warning_wrap("`annotation_height` is set with length of one while with multiple annotations, `annotation_height` is treated as `height`.")

@@ -1090,7 +1106,9 @@ setMethod(f = "re_size",

 				if(length(object@anno_list) == 1 && !inherits(annotation_height, "unit")) {

 					stop_wrap("When there is only one annotation, `annotation_height` should be set as a unit object.")

 				}

-				height = annotation_height[1]

+				if(!inherits(height, "unit")) {

+					height = annotation_height[1]

+				}

 				if(!inherits(height, "unit")) {

 					stop_wrap("`height` should be a `unit` object")

 				}

@@ -1121,6 +1139,11 @@ setMethod(f = "re_size",

 		if(is.null(annotation_width)) {

 			is_annotation_size_set = FALSE

 		} else {

+			if(length(annotation_width) == 1) {

+				if(!inherits(annotation_width, "unit")) {

+					annotation_width = rep(annotation_width, length(object@anno_list))

+				}

+			}

 			if(length(annotation_width) == 1) {

 				if(length(object@anno_list) > 1) {

 					warning_wrap("`annotation_width` is set with length of one while with multiple annotations, `annotation_width` is treated as `width`.")

@@ -1128,7 +1151,9 @@ setMethod(f = "re_size",

 				if(length(object@anno_list) == 1 && !inherits(annotation_width, "unit")) {

 					stop_wrap("When there is only one annotation, `annotation_width` should be set as a unit object.")

 				}

-				width = annotation_width[1]

+				if(!inherits(width, "unit")) {

+					width = annotation_width[1]

+				}

 				if(!inherits(width, "unit")) {

 					stop_wrap("`width` should be a `unit` object")

 				}

@@ -72,16 +72,30 @@ default_col = function(x, main_matrix = FALSE) {

         return(colors)

     } else if(is.numeric(x)) {

         if(main_matrix) {

-            if(length(unique(x)) > 100) {

-                q1 = quantile(x, 0.01)

-                q2 = quantile(x, 0.99)

-                if(length(unique(x[x > q1 & x < q2])) == 1) {

-                     col_fun = colorRamp2(seq(min(x), max(x), length = 3), c("blue", "#EEEEEE", "red"))

+            p = sum(x > 0)/length(x)

+            if(p > 0.3 & p < 0.7) {

+                if(ht_opt$verbose) {

+                    cat("This matrix has both negative and positive values, use a color mapping symmetric to zero\n")

+                }

+                if(length(unique(x)) >= 100) {

+                    q1 = quantile(abs(x), 0.99)

+                    col_fun = colorRamp2(c(-q1, 0, q1), c("blue", "#EEEEEE", "red"))

                 } else {

-                    col_fun = colorRamp2(seq(q1, q2, length = 3), c("blue", "#EEEEEE", "red"))

+                    q1 = max(abs(x))

+                    col_fun = colorRamp2(c(-q1, 0, q1), c("blue", "#EEEEEE", "red"))

                 }

             } else {

-                col_fun = colorRamp2(seq(min(x), max(x), length = 3), c("blue", "#EEEEEE", "red"))

+                if(length(unique(x)) >= 100) {

+                    q1 = quantile(x, 0.01)

+                    q2 = quantile(x, 0.99)

+                    if(length(unique(x[x > q1 & x < q2])) == 1) {

+                         col_fun = colorRamp2(seq(min(x), max(x), length = 3), c("blue", "#EEEEEE", "red"))

+                    } else {

+                        col_fun = colorRamp2(seq(q1, q2, length = 3), c("blue", "#EEEEEE", "red"))

+                    }

+                } else {

+                    col_fun = colorRamp2(seq(min(x), max(x), length = 3), c("blue", "#EEEEEE", "red"))

+                }

             }

         } else {

             #col_fun = colorRamp2(range(min(x), max(x)), c("white", hsv(runif(1), 1, 1)))

@@ -35,7 +35,7 @@ Legend(at, labels = at, col_fun, nrow = NULL, ncol = 1, by_row = FALSE,

   \item{background}{Background colors for the grids. It is used when points and lines are the legend graphics.}

   \item{type}{Type of legends. The value can be one of \code{grid}, \code{points} and \code{lines}.}

   \item{legend_gp}{Graphic parameters for the legend grids. You should control the filled color of the legend grids by \code{gpar(fill = ...)}.}

-  \item{pch}{Type of points if points are used as legend. Note you can use single-letter as pch, e.g. \code{pch = 'A'}.}

+  \item{pch}{Type of points if points are used as legend. Note you can use single-letter as pch, e.g. \code{pch = 'A'}. There are three additional integers that are valid for \code{pch}: 26 and 27 for single diagonal lines and 28 for double diagonal lines.}

   \item{size}{Size of points.}

   \item{legend_height}{Height of the whole legend body. It is only used for vertical continous legend.}

   \item{legend_width}{Width of the whole legend body. It is only used for horizontal continous legend.}

@@ -11,7 +11,7 @@ oncoPrint(mat,

     get_type = default_get_type,

     alter_fun,

     alter_fun_is_vectorized = NULL,

-    col,

+    col = NULL,

     top_annotation = HeatmapAnnotation(cbar = anno_oncoprint_barplot()),

     right_annotation = rowAnnotation(rbar = anno_oncoprint_barplot()),

@@ -14,7 +14,7 @@ Resize the Width or Height of Heatmap Annotations

     height = NULL,

     width = NULL,

     anno_simple_size = ht_opt$anno_simple_size,

-    simple_anno_size_adjust = FALSE)

+    simple_anno_size_adjust = NULL)

 }

 \arguments{