@@ -2,6 +2,7 @@ CHANGES in VERSION 2.1.1

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

 * `anno_mark()`: text positions are correctly calculated now with rotations.

+* The order of legend labels are ordered by either `sort` or `levels`.

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

@@ -350,8 +350,12 @@ Heatmap = function(matrix, col, name,

         warning_wrap("The input is a data frame, convert it to the matrix.")

         matrix = as.matrix(matrix)

     }

+    fa_level = NULL

     if(!is.matrix(matrix)) {

         if(is.atomic(matrix)) {

+            if(is.factor(matrix)) {

+                fa_level = levels(matrix)

+            }

             rn = names(matrix)

             matrix = matrix(matrix, ncol = 1)

             if(!is.null(rn)) rownames(matrix) = rn

@@ -503,6 +507,9 @@ Heatmap = function(matrix, col, name,

     if(ncol(matrix) > 0 && nrow(matrix) > 0) {

         if(missing(col)) {

             col = default_col(matrix, main_matrix = TRUE)

+            if(!is.null(fa_level)) {

+                col = col[fa_level]

+            }

             if(verbose) qqcat("color is not specified, use randomly generated colors\n")

         }

         if(is.function(col)) {

@@ -511,7 +518,11 @@ Heatmap = function(matrix, col, name,

         } else {

             if(is.null(names(col))) {

                 if(length(col) == length(unique(as.vector(matrix)))) {

-                    names(col) = sort(unique(as.vector(matrix)))

+                    if(is.null(fa_level)) {

+                        names(col) = sort(unique(as.vector(matrix)))

+                    } else {

+                        names(col) = fa_level

+                    }

                     .Object@matrix_color_mapping = ColorMapping(colors = col, name = name, na_col = na_col)

                     if(verbose) qqcat("input color is a vector with no names, treat it as discrete color mapping\n")

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

@@ -523,7 +534,11 @@ Heatmap = function(matrix, col, name,

                     stop_wrap("`col` should have names to map to values in `mat`.")

                 }

             } else {

-                col = col[intersect(c(names(col), "_NA_"), as.character(matrix))]

+                if(is.null(fa_level)) {

+                    col = col[intersect(c(names(col), "_NA_"), as.character(matrix))]

+                } else {

+                    col = col[intersect(c(fa_level, "_NA_"), names(col))]

+                }

                 .Object@matrix_color_mapping = ColorMapping(colors = col, name = name, na_col = na_col)

                 if(verbose) qqcat("input color is a named vector\n")

             }

@@ -198,7 +198,10 @@ SingleAnnotation = function(name, value, col, fun,

     .Object@is_anno_matrix = FALSE

     use_mat_column_names = FALSE

+            

     if(!missing(value)) {

+        value2 = value

+    

         if(verbose) qqcat("@{name}: annotation value is vector/matrix\n")

         if(is.logical(value)) {

             if(is.matrix(value)) {

@@ -437,13 +440,14 @@ SingleAnnotation = function(name, value, col, fun,

             color_is_random = TRUE

             if(verbose) qqcat("@{name}: use randomly generated colors\n")

     	}

+

     	if(is.atomic(col)) {

     	    if(is.null(names(col))) {

-                if(is.factor(value)) {

-                    names(col) = levels(value)

+                if(is.factor(value2)) {

+                    names(col) = levels(value2)

                     if(verbose) qqcat("@{names}: add names for discrete color mapping\n")

                 } else if(length(col) == length(unique(value))) {

-                    names(col) = unique(value)

+                    names(col) = sort(unique(value))

                     if(verbose) qqcat("@{names}: add names for discrete color mapping\n")

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

                     col = colorRamp2(seq(min(value, na.rm = TRUE), max(value, na.rm = TRUE), length = length(col)), col)

@@ -453,7 +457,11 @@ SingleAnnotation = function(name, value, col, fun,

             if(is.function(col)) {

                 color_mapping = ColorMapping(name = name, col_fun = col, na_col = na_col)

             } else {

-                col = col[intersect(c(names(col), "_NA_"), as.character(value))]

+                if(is.factor(value2)) {

+                    col = col[intersect(c(levels(value2), "_NA_"), names(col))]

+                } else {

+                    col = col[intersect(c(sort(names(col)), "_NA_"), as.character(value))]

+                }

         		if("_NA_" %in% names(col)) {

         			na_col = col["_NA_"]

         			col = col[names(col) != "_NA_"]