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guess which automatically for HeatmapAnnotation #1140

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guess which automatically for HeatmapAnnotation #1140

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12 changes: 9 additions & 3 deletions R/Heatmap-class.R
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Original file line number Diff line number Diff line change
Expand Up @@ -833,6 +833,12 @@ Heatmap = function(matrix, col, name,
.Object@column_dend_param$cluster_slices = cluster_column_slices

######### annotations #############
# the `top_annotation` will only be evaluated here due to the lazy
# evaluation, we set `.ENV$current_annotation_which` in order to
# HeatmapAnnotation can automatically set its `which` argument.
# the same will be applied for bottom, left, right annotation
old = set_annotation_which("column") # return the initial value
on.exit(set_annotation_which(old), add = TRUE)
.Object@top_annotation = top_annotation # a `HeatmapAnnotation` object
if(is.null(top_annotation)) {
.Object@top_annotation_param$height = unit(0, "mm")
Expand All @@ -858,7 +864,7 @@ Heatmap = function(matrix, col, name,
if(!is.null(top_annotation)) {
validate_anno_names_with_matrix(matrix, top_annotation, "column")
}

set_annotation_which("column")
.Object@bottom_annotation = bottom_annotation # a `HeatmapAnnotation` object
if(is.null(bottom_annotation)) {
.Object@bottom_annotation_param$height = unit(0, "mm")
Expand All @@ -884,7 +890,7 @@ Heatmap = function(matrix, col, name,
if(!is.null(bottom_annotation)) {
validate_anno_names_with_matrix(matrix, bottom_annotation, "column")
}

set_annotation_which("row")
.Object@left_annotation = left_annotation # a `rowAnnotation` object
if(is.null(left_annotation)) {
.Object@left_annotation_param$width = unit(0, "mm")
Expand All @@ -910,7 +916,7 @@ Heatmap = function(matrix, col, name,
if(!is.null(left_annotation)) {
validate_anno_names_with_matrix(matrix, left_annotation, "row")
}

set_annotation_which("row")
.Object@right_annotation = right_annotation # a `rowAnnotation` object
if(is.null(right_annotation)) {
.Object@right_annotation_param$width = unit(0, "mm")
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8 changes: 3 additions & 5 deletions R/HeatmapAnnotation-class.R
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Expand Up @@ -125,12 +125,10 @@ HeatmapAnnotation = function(...,
is_width_set = !missing(width)
is_annotation_height_set = !missing(annotation_height)
is_annotation_width_set = !missing(annotation_width)

.ENV$current_annotation_which = NULL
which = match.arg(which)[1]
.ENV$current_annotation_which = which
which = get_annotation_which(which)
old = set_annotation_which(which) # return the initial value
on.exit({
.ENV$current_annotation_which <- NULL
.ENV$current_annotation_which <- old
dev.off2()
})

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2 changes: 1 addition & 1 deletion R/global.R
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Expand Up @@ -233,7 +233,7 @@ ht_opt = setGlobalOptions(
ht_global_opt = function(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE) {}
ht_global_opt = ht_opt

.ENV = new.env()
.ENV = new.env(parent = emptyenv())
.ENV$current_annotation_which = NULL
.ENV$row_order = NULL
.ENV$row_pos = NULL
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14 changes: 14 additions & 0 deletions R/utils.R
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Expand Up @@ -57,6 +57,20 @@ increase_color_mapping_index = function() {
INDEX_ENV$I_COLOR_MAPPING = INDEX_ENV$I_COLOR_MAPPING + 1
}

get_annotation_which = function(which) {
out = .ENV$current_annotation_which
if(is.null(out)) {
out = match.arg(which, c("column", "row"))
}
out
}

set_annotation_which = function(which) {
old = .ENV$current_annotation_which
.ENV$current_annotation_which = which
invisible(old)
}

# default colors for matrix or annotations
# this function should be improved later
default_col = function(x, main_matrix = FALSE) {
Expand Down