R/decorate.R

In ComplexHeatmap: Make Complex Heatmaps

# == title
# Decorate Heatmap Bodies
#
# == param
# -heatmap Name of the heatmap which is set as ``name`` argument in `Heatmap` function.
# -code Code that adds graphics in the selected heatmap body.
# -slice Index of the row slice in the heatmap.
# -row_slice Index of the row slice in the heatmap.
# -column_slice Index of the column slice in the heatmap.
# -envir Where to look for variables inside ``code``.
#
# == details
# There is a viewport for each slice in each heatmap.
# This function contructs the name of the viewport,
# goes to the viewport by `grid::seekViewport`, runs the code
# to that viewport and finally goes back to the original viewport.
#
# == value
# This function returns no value.
#
# == seealso
# https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# set.seed(123)
# Heatmap(matrix(rnorm(100), 10), name = "mat")
# decorate_heatmap_body("mat", {
#     grid.circle(gp = gpar(fill = "#FF000080"))
# })
#
decorate_heatmap_body = function(heatmap, code, 
	slice = 1, row_slice = slice, column_slice = 1,
	envir = new.env(parent = parent.frame())) {

	current_vp = current.viewport()$name
	if(current_vp == "ROOT") {
		current_vp = "global"
	}
	
	vp_name = paste0(heatmap, "_heatmap_body_", row_slice, "_", column_slice)
	seekViewport(vp_name)

	eval(substitute(code), envir = envir)

	seekViewport(current_vp)
}

# == title
# Decorate Heatmap Dendrograms
#
# == param
# -heatmap Name of the heatmap.
# -code Code that adds graphics in the selected heatmap dendrogram.
# -slice Index of the row slice or column slice in the heatmap.
# -which Is the dendrogram on rows or on columns?
# -envir Where to look for variables inside ``code``.
#
# == details
#
# If you know the number of leaves in the dendrogram, it is
# simple to calculate the position of every leave in the dendrogram.
# E.g., for the column dendrogram, the i^th leave is located at:
#
#     # assume nc is the number of columns in the column slice
#     unit((i-0.5)/nc, "npc")
#
#
# == value
# This function returns no value.
#
# == seealso
# https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# set.seed(123)
# Heatmap(matrix(rnorm(100), 10), name = "mat", km = 2)
# decorate_dend("mat", {
#     grid.rect(gp = gpar(fill = "#FF000080"))
# }, which = "row", slice = 2)
#
decorate_dend = function(heatmap, code, slice = 1, which = c("column", "row"), 
	envir = new.env(parent = parent.frame())) {
	
	current_vp = current.viewport()$name
	if(current_vp == "ROOT") {
		current_vp = "global"
	}

	which = match.arg(which)[1]
	vp_name = paste0(heatmap, "_dend_", which, "_", slice)	
	seekViewport(vp_name)
	e = new.env(parent = parent.frame())
	eval(substitute(code), envir = envir)

	seekViewport(current_vp)
}

# == title
# Decorate Heatmap Column Dendrograms
#
# == 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`.
#
# == value
# The function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
decorate_column_dend = function(..., envir = new.env(parent = parent.frame())) {
	decorate_dend(..., which = "column", envir = envir)
}

# == title
# Decorate Heatmap Row Dendrograms
#
# == 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`.
#
# == value
# The function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
decorate_row_dend = function(..., envir = new.env(parent = parent.frame())) {
	decorate_dend(..., which = "row", envir = envir)
}


# == title
# Decorate Heatmap Dimension Names
#
# == param
# -heatmap Name of the heatmap.
# -code Code that adds graphics in the selected viewport.
# -slice Index of the row slice or column slice in the heatmap.
# -which on rows or on columns?
# -envir where to look for variables inside ``code``.
#
# == details
# If you know the dimensions of the matrix, it is
# simple to calculate the position of every row name or column name in the heatmap.
# E.g., for the column column, the i^th name is located at:
#
#     # assume nc is the number of columns in the column slice
#     unit((i-0.5)/nc, "npc")
#
#
# == value
# The function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# set.seed(123)
# mat = matrix(rnorm(100), 10)
# rownames(mat) = letters[1:10]
# colnames(mat) = LETTERS[1:10]
# Heatmap(mat, name = "mat", km = 2)
# 
# decorate_dimnames("mat", {
#     grid.rect(gp = gpar(fill = "#FF000080"))
# }, which = "row", slice = 2)
#
decorate_dimnames = function(heatmap, code, slice = 1, which = c("column", "row"), 
	envir = new.env(parent = parent.frame())) {
	
	current_vp = current.viewport()$name
	if(current_vp == "ROOT") {
		current_vp = "global"
	}

	which = match.arg(which)[1]
	vp_name = paste0(heatmap, "_", which, "_names_", slice)
	seekViewport(vp_name)
	eval(substitute(code), envir = envir)
	seekViewport(current_vp)
}

# == title
# Decorate Heatmap Row Names
#
# == param
# -... Pass to `decorate_dimnames`.
# -envir wWhere to look for variables inside ``code``.
#
# == details
# This is a helper function which pre-defined ``which`` argument in `decorate_dimnames`.
#
# == value
# The function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
decorate_row_names = function(..., envir = new.env(parent = parent.frame())) {
	decorate_dimnames(..., which = "row", envir = envir)
}

# == title
# Decorate Heatmap Column Names
#
# == 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`.
#
# == value
# The function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
decorate_column_names = function(..., envir = new.env(parent = parent.frame())) {
	decorate_dimnames(..., which = "column", envir = envir)
}


# == title
# Decorate Heatmap Titles
#
# == param
# -heatmap Name of the heatmap.
# -code Code that adds graphics in the selected viewport.
# -slice Index of the row slice or column slice in the heatmap.
# -which Is it a row title or a column title?
# -envir Where to look for variables inside ``code``.
#
# == details
# There is a viewport for row titles and column title in the heatmap.
# This function contructs the name of the viewport,
# goes to the viewport by `grid::seekViewport` , runs code
# to that viewport and finally goes back to the original viewport.
#
# == value
# The function returns no value.
#
# == seealso
# https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# set.seed(123)
# Heatmap(matrix(rnorm(100), 10), name = "mat", km = 2)
# decorate_title("mat", {
#     grid.rect(gp = gpar(fill = "#FF000080"))
# }, which = "row", slice = 2)
#
decorate_title = function(heatmap, code, slice = 1, which = c("column", "row"), 
	envir = new.env(parent = parent.frame())) {
	
	current_vp = current.viewport()$name
	if(current_vp == "ROOT") {
		current_vp = "global"
	}

	which = match.arg(which)[1]
	vp_name = paste0(heatmap, "_", which, "_title_", slice)
	seekViewport(vp_name)
	eval(substitute(code), envir = envir)
	seekViewport(current_vp)
}

# == title
# Decorate Heatmap Row Titles
#
# == 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`.
#
# == value
# The function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
decorate_row_title = function(..., envir = new.env(parent = parent.frame())) {
	decorate_title(..., which = "row", envir = envir)
}

# == title
# Decorate Heatmap Column Titles
#
# == 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`.
#
# == value
# The function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
decorate_column_title = function(..., envir = new.env(parent = parent.frame())) {
	decorate_title(..., which = "column", envir = envir)
}

# == title
# Decorate Heatmap Annotation
#
# == param
# -annotation Name of the annotation.
# -code Code that adds graphics in the selected heatmap annotation.
# -slice Index of the row slices or the column slice in the heatmap.
# -envir Where to look for variables inside ``code``.
#
# == details
# There is a viewport for every column annotation and row annotation.
# This function contructs the name of the viewport,
# goes to the viewport by `grid::seekViewport`, runs code
# to that viewport, and finally goes back to the original viewport.
#
# == value
# The function returns no value.
#
# == seealso
# https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# set.seed(123)
# ha1 = HeatmapAnnotation(df = data.frame(type = rep(letters[1:2], 5)))
# ha2 = rowAnnotation(point = anno_points(runif(10), which = "row"))
# Heatmap(matrix(rnorm(100), 10), name = "mat", km = 2,
#     top_annotation = ha1) + ha2
# decorate_annotation("type", {
#     grid.circle(x = unit(c(0.2, 0.4, 0.6, 0.8), "npc"), 
#         gp = gpar(fill = "#FF000080"))
# })
# decorate_annotation("point", {
#     grid.rect(gp = gpar(fill = "#FF000080"))
# }, slice = 2)
#
decorate_annotation = function(annotation, code, slice = 1, envir = new.env(parent = parent.frame())) {

	current_vp = current.viewport()$name
	if(current_vp == "ROOT") {
		current_vp = "global"
	}
	
	vp_name = paste0("annotation_", annotation, "_", slice)
	seekViewport(vp_name)
	eval(substitute(code), envir = envir)
	seekViewport(current_vp)
}