@@ -7,6 +7,7 @@ CHANGES in VERSION 1.13.1

 * `HeatmapAnnotation()`: gaps are included in the size of the annotations

 * `anno_link()`: graphic parameters are correctly reordered

 * `densityHeatmap()`: viewport is created with `clip = TRUE`

+* `decorate_*()`: add `envir` option to control where to look for variables inside `code`

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

@@ -5,6 +5,7 @@

 # -heatmap name of the heatmap which is set as ``name`` option in `Heatmap` function

 # -code code that adds graphics in the selected heatmap body

 # -slice index of row slices in the heatmap if it is split by rows

+# -envir where to look for variables inside ``code``

 #

 # == details

 # There is a viewport for each row slice in each heatmap.

@@ -41,7 +42,7 @@

 #     grid.circle(gp = gpar(fill = "#FF000080"))

 # })

 #

-decorate_heatmap_body = function(heatmap, code, slice = 1) {

+decorate_heatmap_body = function(heatmap, code, slice = 1, envir = new.env(parent = parent.frame())) {

 	if(is.null(slice)) {

 		vp_name = paste0(heatmap, "_heatmap_body_", 1)

@@ -52,8 +53,7 @@ decorate_heatmap_body = function(heatmap, code, slice = 1) {

 		seekViewport(vp_name)

 	}

-	e = new.env(parent = parent.frame())

-	eval(substitute(code), envir = e)

+	eval(substitute(code), envir = envir)

 	seekViewport("global")

 }

@@ -66,6 +66,7 @@ decorate_heatmap_body = function(heatmap, code, slice = 1) {

 # -code code that adds graphics in the selected heatmap body

 # -slice index of row slices in the heatmap

 # -which on rows or on columns?

+# -envir where to look for variables inside ``code``

 #

 # == details

 # There is a viewport for each dendrogram in the heatmap.

@@ -94,7 +95,8 @@ decorate_heatmap_body = function(heatmap, code, slice = 1) {

 #     grid.rect(gp = gpar(fill = "#FF000080"))

 # }, which = "row", slice = 2)

 #

-decorate_dend = function(heatmap, code, slice = 1, which = c("column", "row")) {

+decorate_dend = function(heatmap, code, slice = 1, which = c("column", "row"), 

+	envir = new.env(parent = parent.frame())) {

 	which = match.arg(which)[1]

 	if(which == "column") {

@@ -122,6 +124,7 @@ decorate_dend = function(heatmap, code, slice = 1, which = c("column", "row")) {

 #

 # == param

 # -... pass to `decorate_dend`

+# -envir where to look for variables inside ``code``

 #

 # == details

 # This is a wrapper function which pre-defined ``which`` argument in `decorate_dend`.

@@ -136,8 +139,8 @@ decorate_dend = function(heatmap, code, slice = 1, which = c("column", "row")) {

 # # No example for this function

 # NULL

 #

-decorate_column_dend = function(...) {

-	decorate_dend(..., which = "column")

+decorate_column_dend = function(..., envir = new.env(parent = parent.frame())) {

+	decorate_dend(..., which = "column", envir = envir)

 }

 # == title

@@ -145,6 +148,7 @@ decorate_column_dend = function(...) {

 #

 # == param

 # -... pass to `decorate_dend`

+# -envir where to look for variables inside ``code``

 #

 # == details

 # This is a helper function which pre-defined ``which`` argument in `decorate_dend`.

@@ -159,8 +163,8 @@ decorate_column_dend = function(...) {

 # # No example for this function

 # NULL

 #

-decorate_row_dend = function(...) {

-	decorate_dend(..., which = "row")

+decorate_row_dend = function(..., envir = new.env(parent = parent.frame())) {

+	decorate_dend(..., which = "row", envir = envir)

 }

@@ -172,6 +176,7 @@ decorate_row_dend = function(...) {

 # -code code that adds graphics in the selected heatmap body

 # -slice index of row slices in the heatmap

 # -which on rows or on columns?

+# -envir where to look for variables inside ``code``

 #

 # == details

 # There is a viewport for row names and column names in the heatmap.

@@ -204,7 +209,8 @@ decorate_row_dend = function(...) {

 #     grid.rect(gp = gpar(fill = "#FF000080"))

 # }, which = "row", slice = 2)

 #

-decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row")) {

+decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row"), 

+	envir = new.env(parent = parent.frame())) {

 	which = match.arg(which)[1]

 	if(which == "column") {

@@ -221,8 +227,7 @@ decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row"

 	}

 	seekViewport(vp_name)

-	e = new.env(parent = parent.frame())

-	eval(substitute(code), envir = e)

+	eval(substitute(code), envir = envir)

 	seekViewport("global")

 }

@@ -231,6 +236,7 @@ decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row"

 #

 # == param

 # -... pass to `decorate_dimnames`

+# -envir where to look for variables inside ``code``

 #

 # == details

 # This is a helper function which pre-defined ``which`` argument in `decorate_dimnames`.

@@ -245,8 +251,8 @@ decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row"

 # # No example for this function

 # NULL

 #

-decorate_row_names = function(...) {

-	decorate_dimnames(..., which = "row")

+decorate_row_names = function(..., envir = new.env(parent = parent.frame())) {

+	decorate_dimnames(..., which = "row", envir = envir)

 }

 # == title

@@ -254,6 +260,7 @@ decorate_row_names = function(...) {

 #

 # == param

 # -... pass to `decorate_dimnames`

+# -envir where to look for variables inside ``code``

 #

 # == details

 # This is a helper function which pre-defined ``which`` argument in `decorate_dimnames`.

@@ -268,8 +275,8 @@ decorate_row_names = function(...) {

 # # No example for this function

 # NULL

 #

-decorate_column_names = function(...) {

-	decorate_dimnames(..., which = "column")

+decorate_column_names = function(..., envir = new.env(parent = parent.frame())) {

+	decorate_dimnames(..., which = "column", envir = envir)

 }

@@ -281,6 +288,7 @@ decorate_column_names = function(...) {

 # -code code that adds graphics in the selected heatmap body

 # -slice index of row slices in the heatmap

 # -which on rows or on columns?

+# -envir where to look for variables inside ``code``

 #

 # == details

 # There is a viewport for row titles and column title in the heatmap.

@@ -301,7 +309,8 @@ decorate_column_names = function(...) {

 #     grid.rect(gp = gpar(fill = "#FF000080"))

 # }, which = "row", slice = 2)

 #

-decorate_title = function(heatmap, code, slice = 1, which = c("column", "row")) {

+decorate_title = function(heatmap, code, slice = 1, which = c("column", "row"), 

+	envir = new.env(parent = parent.frame())) {

 	which = match.arg(which)[1]

 	if(which == "column") {

@@ -318,8 +327,7 @@ decorate_title = function(heatmap, code, slice = 1, which = c("column", "row"))

 	}

 	seekViewport(vp_name)

-	e = new.env(parent = parent.frame())

-	eval(substitute(code), envir = e)

+	eval(substitute(code), envir = envir)

 	seekViewport("global")

 }

@@ -328,6 +336,7 @@ decorate_title = function(heatmap, code, slice = 1, which = c("column", "row"))

 #

 # == param

 # -... pass to `decorate_title`

+# -envir where to look for variables inside ``code``

 #

 # == details

 # This is a helper function which pre-defined ``which`` argument in `decorate_title`.

@@ -342,8 +351,8 @@ decorate_title = function(heatmap, code, slice = 1, which = c("column", "row"))

 # # No example for this function

 # NULL

 #

-decorate_row_title = function(...) {

-	decorate_title(..., which = "row")

+decorate_row_title = function(..., envir = new.env(parent = parent.frame())) {

+	decorate_title(..., which = "row", envir = envir)

 }

 # == title

@@ -351,6 +360,7 @@ decorate_row_title = function(...) {

 #

 # == param

 # -... pass to `decorate_title`

+# -envir where to look for variables inside ``code``

 #

 # == details

 # This is a helper function which pre-defined ``which`` argument in `decorate_title`.

@@ -365,8 +375,8 @@ decorate_row_title = function(...) {

 # # No example for this function

 # NULL

 #

-decorate_column_title = function(...) {

-	decorate_title(..., which = "column")

+decorate_column_title = function(..., envir = new.env(parent = parent.frame())) {

+	decorate_title(..., which = "column", envir = envir)

 }

 # == title

@@ -376,6 +386,7 @@ decorate_column_title = function(...) {

 # -annotation name of the annotation

 # -code code that adds graphics in the selected heatmap body

 # -slice index of row slices in the heatmap

+# -envir where to look for variables inside ``code``

 #

 # == details

 # There is a viewport for every column annotation and row annotation.

@@ -403,7 +414,7 @@ decorate_column_title = function(...) {

 #     grid.rect(gp = gpar(fill = "#FF000080"))

 # }, slice = 2)

 #

-decorate_annotation = function(annotation, code, slice) {

+decorate_annotation = function(annotation, code, slice, envir = new.env(parent = parent.frame())) {

 	if(missing(slice)) {

 		vp_name = paste0("annotation_", annotation)

@@ -428,8 +439,7 @@ decorate_annotation = function(annotation, code, slice) {

 		}

 	}

-	e = new.env(parent = parent.frame())

-	eval(substitute(code), envir = e)

+	eval(substitute(code), envir = envir)

 	seekViewport("global")

 }

@@ -7,13 +7,14 @@ Decorate the heatmap annotation

 Decorate the heatmap annotation

 }

 \usage{

-decorate_annotation(annotation, code, slice)

+decorate_annotation(annotation, code, slice, envir = new.env(parent = parent.frame()))

 }

 \arguments{

   \item{annotation}{name of the annotation}

   \item{code}{code that adds graphics in the selected heatmap body}

   \item{slice}{index of row slices in the heatmap}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,11 +7,12 @@ Decorate heatmap dendrogram on columns

 Decorate heatmap dendrogram on columns

 }

 \usage{

-decorate_column_dend(...)

+decorate_column_dend(..., envir = new.env(parent = parent.frame()))

 }

 \arguments{

   \item{...}{pass to \code{\link{decorate_dend}}}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,11 +7,12 @@ Decorate heatmap column names

 Decorate heatmap column names

 }

 \usage{

-decorate_column_names(...)

+decorate_column_names(..., envir = new.env(parent = parent.frame()))

 }

 \arguments{

   \item{...}{pass to \code{\link{decorate_dimnames}}}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,11 +7,12 @@ Decorate heatmap column title

 Decorate heatmap column title

 }

 \usage{

-decorate_column_title(...)

+decorate_column_title(..., envir = new.env(parent = parent.frame()))

 }

 \arguments{

   \item{...}{pass to \code{\link{decorate_title}}}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,7 +7,8 @@ Decorate the heatmap dendrogram

 Decorate the heatmap dendrogram

 }

 \usage{

-decorate_dend(heatmap, code, slice = 1, which = c("column", "row"))

+decorate_dend(heatmap, code, slice = 1, which = c("column", "row"),

+    envir = new.env(parent = parent.frame()))

 }

 \arguments{

@@ -15,6 +16,7 @@ decorate_dend(heatmap, code, slice = 1, which = c("column", "row"))

   \item{code}{code that adds graphics in the selected heatmap body}

   \item{slice}{index of row slices in the heatmap}

   \item{which}{on rows or on columns?}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,7 +7,8 @@ Decorate the heatmap dimension names

 Decorate the heatmap dimension names

 }

 \usage{

-decorate_dimnames(heatmap, code, slice = 1, which = c("column", "row"))

+decorate_dimnames(heatmap, code, slice = 1, which = c("column", "row"),

+    envir = new.env(parent = parent.frame()))

 }

 \arguments{

@@ -15,6 +16,7 @@ decorate_dimnames(heatmap, code, slice = 1, which = c("column", "row"))

   \item{code}{code that adds graphics in the selected heatmap body}

   \item{slice}{index of row slices in the heatmap}

   \item{which}{on rows or on columns?}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,13 +7,14 @@ Decorate the heatmap body

 Decorate the heatmap body

 }

 \usage{

-decorate_heatmap_body(heatmap, code, slice = 1)

+decorate_heatmap_body(heatmap, code, slice = 1, envir = new.env(parent = parent.frame()))

 }

 \arguments{

   \item{heatmap}{name of the heatmap which is set as \code{name} option in \code{\link{Heatmap}} function}

   \item{code}{code that adds graphics in the selected heatmap body}

   \item{slice}{index of row slices in the heatmap if it is split by rows}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,11 +7,12 @@ Decorate heatmap dendrogram on rows

 Decorate heatmap dendrogram on rows

 }

 \usage{

-decorate_row_dend(...)

+decorate_row_dend(..., envir = new.env(parent = parent.frame()))

 }

 \arguments{

   \item{...}{pass to \code{\link{decorate_dend}}}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,11 +7,12 @@ Decorate heatmap row names

 Decorate heatmap row names

 }

 \usage{

-decorate_row_names(...)

+decorate_row_names(..., envir = new.env(parent = parent.frame()))

 }

 \arguments{

   \item{...}{pass to \code{\link{decorate_dimnames}}}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,11 +7,12 @@ Decorate heatmap row title

 Decorate heatmap row title

 }

 \usage{

-decorate_row_title(...)

+decorate_row_title(..., envir = new.env(parent = parent.frame()))

 }

 \arguments{

   \item{...}{pass to \code{\link{decorate_title}}}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{

@@ -7,7 +7,8 @@ Decorate the heatmap title

 Decorate the heatmap title

 }

 \usage{

-decorate_title(heatmap, code, slice = 1, which = c("column", "row"))

+decorate_title(heatmap, code, slice = 1, which = c("column", "row"),

+    envir = new.env(parent = parent.frame()))

 }

 \arguments{

@@ -15,6 +16,7 @@ decorate_title(heatmap, code, slice = 1, which = c("column", "row"))

   \item{code}{code that adds graphics in the selected heatmap body}

   \item{slice}{index of row slices in the heatmap}

   \item{which}{on rows or on columns?}

+  \item{envir}{where to look for variables inside \code{code}}

 }

 \details{