@@ -5,7 +5,7 @@ Version: 1.4.2

 Date: 2015-9-14

 Author: Zuguang Gu

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

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

+Depends: R (>= 3.1.0), grid, graphics, stats, grDevices

 Imports: methods, circlize (>= 0.3.1), GetoptLong, colorspace,

     RColorBrewer, dendextend (>= 1.0.1), GlobalOptions (>= 0.0.6)

 Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust, 

@@ -1,5 +1,6 @@

 CHANGES in VERSION 1.4.2

+* order of annotations can be adjusted arbitrarily

 * anno_barplot: scales are adjusted according to the baseline

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

@@ -67,7 +67,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 #

 HeatmapAnnotation = function(df, name, col, 

 	annotation_legend_param = list(), 

-	show_legend = rep(TRUE, n_anno), 

+	show_legend = TRUE, 

 	..., 

 	which = c("column", "row"), 

 	annotation_height = 1, 

@@ -90,84 +90,117 @@ HeatmapAnnotation = function(df, name, col,

 	.Object@name = name

 	n_anno = 0

-	if(!missing(df)) {

-		if(is.null(colnames(df))) {

-	        stop("`df` should have column names.")

-	    }

-

-	    anno_name = colnames(df)

-	    n_anno = ncol(df)

-

-	    if(length(show_legend) == 1) {

-	    	show_legend = rep(show_legend, n_anno)

-	    }

-

-	    if(length(annotation_legend_param) == 0) {

-	    	annotation_legend_param = rep.list(NULL, n_anno)

-	    } else if(inherits(annotation_legend_param, "list")) {

-	    	if(all(sapply(annotation_legend_param, inherits, "list"))) {  # if it is a list of lists

-	    		nl = length(annotation_legend_param)

-	    		if(nl > n_anno) {

-	    			stop("Amount of legend params is larger than the number of simple annotations.")

-	    		}

-	    		if(is.null(names(annotation_legend_param))) {

-	    			names(annotation_legend_param) = anno_name[seq_len(nl)]

-	    		} else if(length(setdiff(names(annotation_legend_param), anno_name))) {

-	    			stop("Some names in 'annotation_legend_param' are not in names of simple annotations.")

-	    		} else {

-	    			annotation_legend_param = annotation_legend_param[ intersect(anno_name, names(annotation_legend_param)) ]

-	    		}

-	    		lp = rep.list(NULL, n_anno)

-

-	    		names(lp) = anno_name

-	    		for(i in seq_along(lp)) {

-	    			lp[[i]] = annotation_legend_param[[i]]

-	    		}

-	    		annotation_legend_param = lp

-	    	} else {

-	    		annotation_legend_param = rep.list(annotation_legend_param, n_anno)

-	    	}

-	    }

-

-

-	    if(missing(col)) {

-	        for(i in seq_len(n_anno)) {

-	        	anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i], gp = gp, legend_param = annotation_legend_param[[i]])))

-	        }

-	    } else {

-	        for(i in seq_len(n_anno)) {

-	        	if(is.null(col[[ anno_name[i] ]])) { # if the color is not provided

-	        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i], gp = gp, legend_param = annotation_legend_param[[i]])))

-	        	} else {

-	        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], col = col[[ anno_name[i] ]], which = which, show_legend = show_legend[i], gp = gp, legend_param = annotation_legend_param[[i]])))

-	        	}

-	        }

-	    }

+    arg_list = as.list(match.call())[-1]

+    called_args = names(arg_list)

+    anno_args = setdiff(called_args, c("name", "col", "annotation_legend_param", "show_legend", "which", 

+    	                             "annotation_height", "annotation_width", "height", "width", "gp", "gap"))

+    if(any(anno_args == "")) stop("annotations should have names.")

+    if(any(duplicated(anno_args))) stop("names of annotations should be unique.")

+    anno_arg_list = list(...)

+    if(length(anno_arg_list)) {

+	    n_simple_anno = {if("df" %in% anno_args) ncol(df) else 0} + sum(sapply(anno_arg_list, is.atomic))

+	    simple_anno_name = c({if("df" %in% anno_args) colnames(df) else NULL}, anno_args[sapply(anno_arg_list, is.atomic)])

+	} else {

+		n_simple_anno = {if("df" %in% anno_args) ncol(df) else 0}

+	    simple_anno_name = {if("df" %in% anno_args) colnames(df) else NULL}

 	}

-	if(which == "column") {

-		anno_list = rev(anno_list)

+

+    if(any(duplicated(simple_anno_name))) stop("names of simple annotations should be unique.")

+

+    # normalize `show_legend`

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

+		show_legend = rep(show_legend, n_simple_anno)

 	}

-	# self-defined anntatoin graph are passed by a list of named functions

-	fun_list = list(...)

-	if(length(fun_list)) {

-		if(! all(sapply(fun_list, is.function))) {

-			stop("`...` should only contains functions.")

+	# normalize `heatmap_legend_param`

+	if(length(annotation_legend_param) == 0) {

+		annotation_legend_param = rep.list(NULL, n_simple_anno)

+	} else if(inherits(annotation_legend_param, "list")) {

+		if(all(sapply(annotation_legend_param, inherits, "list"))) {  # if it is a list of lists

+			nl = length(annotation_legend_param)

+			if(nl > n_simple_anno) {

+				stop("Amount of legend params is larger than the number of simple annotations.")

+			}

+			if(is.null(names(annotation_legend_param))) {

+				names(annotation_legend_param) = simple_anno_name[seq_len(nl)]

+			} else if(length(setdiff(names(annotation_legend_param), simple_anno_name))) {

+				stop("Some names in 'annotation_legend_param' are not in names of simple annotations.")

+			} else {

+				annotation_legend_param = annotation_legend_param[ intersect(simple_anno_name, names(annotation_legend_param)) ]

+			}

+			lp = rep.list(NULL, n_simple_anno)

+

+			names(lp) = simple_anno_name

+			for(i in seq_along(lp)) {

+				lp[[i]] = annotation_legend_param[[i]]

+			}

+			annotation_legend_param = lp

+		} else {

+			annotation_legend_param = rep.list(annotation_legend_param, n_simple_anno)

 		}

+	}

-		fun_name = names(fun_list)

-		if(is.null(fun_name)) {

-			stop("functions should be specified as named arguments.")

-		}

-		if(any(fun_name %in% c("df", "col", "show_legend", "which", "height", "width", "annotation_height", "annotation_width", "gp", "color_bar"))) {

-			stop("function names should be same as other argument names.")

-		}

-			

-		for(i in seq_along(fun_name)) {

-			anno_list = c(anno_list, list(SingleAnnotation(name = fun_name[i], fun = fun_list[[i]], which = which)))

+	i_simple = 0

+	simple_length = NULL

+    for(ag in anno_args) {

+		if(ag == "df") {

+			if(is.null(colnames(df))) {

+		        stop("`df` should have column names.")

+		    }

+		    if(is.null(simple_length)) {

+		    	simple_length = nrow(df)

+		    } else if(nrow(df) != simple_length) {

+		    	stop("length of simple annotations differ.")

+		    }

+

+		    anno_name = colnames(df)

+		    n_anno = ncol(df)

+

+		    if(missing(col)) {

+		        for(i in seq_len(n_anno)) {

+		        	anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]])))

+		        }

+		    } else {

+		        for(i in seq_len(n_anno)) {

+		        	if(is.null(col[[ anno_name[i] ]])) { # if the color is not provided

+		        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]])))

+		        	} else {

+		        		anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], col = col[[ anno_name[i] ]], which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]])))

+		        	}

+		        }

+		    }

+		    i_simple = i_simple + n_anno

+		} else {

+			if(inherits(anno_arg_list[[ag]], "function")) {

+				anno_list = c(anno_list, list(SingleAnnotation(name = ag, fun = anno_arg_list[[ag]], which = which)))

+			} else if(is.atomic(anno_arg_list[[ag]])) {

+

+			    if(is.null(simple_length)) {

+			    	simple_length = length(anno_arg_list[[ag]])

+			    } else if(length(anno_arg_list[[ag]]) != simple_length) {

+			    	stop("length of simple annotations differ.")

+			    }

+

+				if(missing(col)) {

+			        anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]])))

+			    } else {

+			        if(is.null(col[[ ag ]])) { # if the color is not provided

+			        	anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]])))

+			        } else {

+			        	anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], col = col[[ ag ]], which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]])))

+			        }

+			    }

+			    i_simple = i_simple + 1

+			} else {

+				stop("additional arguments should be annotation vectors or annotation functions.")

+			} 

 		}

 	}

+	if(which == "column") {

+		anno_list = rev(anno_list)

+	}

+

 	n_anno = length(anno_list)

 	if(is.null(gap)) gap = unit(0, "mm")

@@ -9,7 +9,7 @@ Constructor method for HeatmapAnnotation class

 \usage{

 HeatmapAnnotation(df, name, col,

     annotation_legend_param = list(),

-    show_legend = rep(TRUE, n_anno),

+    show_legend = TRUE,

     ...,

     which = c("column", "row"),

     annotation_height = 1,

@@ -89,6 +89,18 @@ ha

 draw(ha, 1:10)

 ```

+Also individual annotations can be specified as vectors:

+

+```{r heatmap_annotation_vector, fig.width = 7, fig.height = 1}

+ha = HeatmapAnnotation(type = c(rep("a", 5), rep("b", 5)),

+                       age = sample(1:20, 10),

+    col = list(type = c("a" = "red", "b" = "blue"),

+               age = colorRamp2(c(0, 20), c("white", "red")))

+)

+ha

+draw(ha, 1:10)

+```

+

 To put column annotation to the heatmap, specify `top_annotation` and `bottom_annotation` in `Heatmap()`.

 ```{r heatmap_column_annotation}

@@ -179,6 +191,19 @@ ha

 draw(ha, 1:10)

 ```

+Since simple annotations can also be specified as vectors, actually you arrange annotations in any order:

+

+```{r, fig.width = 7, fig.height = 2}

+ha = HeatmapAnnotation(type = c(rep("a", 5), rep("b", 5)),

+                       points = anno_points(value),

+                       age = sample(1:20, 10), 

+                       bars = anno_barplot(value),

+    col = list(type = c("a" = "red", "b" = "blue"),

+               age = colorRamp2(c(0, 20), c("white", "red"))))

+ha

+draw(ha, 1:10)

+```

+

 For some of the `anno_*` functions, graphic parameters can be set by `gp` argument.

 Also note how we specify `baseline` in `anno_barplot()`.