-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
27 changed files
with
770 additions
and
552 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -6,3 +6,4 @@ | |
| ^README\.Rmd$ | ||
| ^README\.html$ | ||
| ^\.github$ | ||
| ^README\.zh-cn\.md$ | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| #' Construct HeatmapAnnotation object | ||
| #' | ||
| #' This function is similar to the | ||
| #' [HeatmapAnnotation][ComplexHeatmap::HeatmapAnnotation] function, but it | ||
| #' automatically guesses the `which` argument when combined with the [eheat] | ||
| #' function. Additionally, the `eheat_anno` function provides alternative | ||
| #' options to set the height(or width) of each individual annotation or adjust | ||
| #' the dimensions of the entire set of column/row annotations simultaneously | ||
| #' using the `annotation_size` or `size` parameters. | ||
| #' | ||
| #' @param ... Additional arguments passed to | ||
| #' [HeatmapAnnotation][ComplexHeatmap::HeatmapAnnotation]. | ||
| #' @param annotation_size Height/width of each annotation for column/row | ||
| #' annotation. | ||
| #' @param size Height/width of the whole annotations for column/row annotation. | ||
| #' @param which A string of `"row"` or `"column"`. | ||
| #' @return A [HeatmapAnnotation][ComplexHeatmap::HeatmapAnnotation-class] | ||
| #' object. | ||
| #' @examples | ||
| #' # No need to specify which argument if combine with `ggheat` or `eheat` | ||
| #' g <- ggplot(mpg, aes(displ, hwy, colour = class)) + | ||
| #' geom_point() | ||
| #' m <- matrix(rnorm(100), 10) | ||
| #' ggheat(m, | ||
| #' top_annotation = eheat_anno( | ||
| #' ggplot = anno_gg(g, "panel", | ||
| #' clip = "on", | ||
| #' height = unit(6, "cm"), | ||
| #' show_name = FALSE | ||
| #' ) | ||
| #' ) | ||
| #' ) | ||
| #' @export | ||
| eheat_anno <- function(..., annotation_size = NULL, size = NULL, which = NULL) { | ||
| which <- eheat_which(which) | ||
| old <- eheat_env_set("current_annotation_which", which) | ||
| on.exit(eheat_env_set("current_annotation_which", old), add = TRUE) | ||
| if (!rlang::is_named(dots <- rlang::list2(...))) { | ||
| cli::cli_abort("all arguments must be named") | ||
| } | ||
| if (which == "row") { | ||
| dots$annotation_width <- dots$annotation_width %||% annotation_size | ||
| dots$width <- dots$width %||% size | ||
| if (!is.null(.subset2(dots, "annotation_height"))) { | ||
| cli::cli_warn( | ||
| "cannot set {.arg annotation_height} for row annotation" | ||
| ) | ||
| dots$annotation_height <- NULL | ||
| } | ||
| if (!is.null(.subset2(dots, "height"))) { | ||
| cli::cli_warn("cannot set {.arg height} for row annotation") | ||
| dots$height <- NULL | ||
| } | ||
| } else { | ||
| dots$annotation_height <- dots$annotation_height %||% annotation_size | ||
| dots$height <- dots$height %||% size | ||
| if (!is.null(.subset2(dots, "annotation_width"))) { | ||
| cli::cli_warn( | ||
| "cannot set {.arg annotation_width} for column annotation" | ||
| ) | ||
| dots$annotation_width <- NULL | ||
| } | ||
| if (!is.null(.subset2(dots, "width"))) { | ||
| cli::cli_warn("cannot set {.arg width} for column annotation") | ||
| dots$width <- NULL | ||
| } | ||
| } | ||
| rlang::inject(ComplexHeatmap::HeatmapAnnotation(!!!dots, which = which)) | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,24 +1,14 @@ | ||
| #' Prepare ExtendedHeatmap | ||
| #' | ||
| #' @param object A [ExtendedHeatmap][eheat] or [ExtendedAnnotation][eanno] | ||
| #' object. | ||
| #' @param ... Not used currently. | ||
| #' @return An modified `object` with the same class. | ||
| #' @examples | ||
| #' eheat_prepare(eheat(matrix(rnorm(81), nrow = 9))) | ||
| #' @export | ||
| eheat_prepare <- function(object, ...) { | ||
| UseMethod("eheat_prepare") | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname eheat_prepare | ||
| eheat_prepare.ExtendedHeatmap <- function(object, ...) { | ||
| object | ||
| } | ||
| #' # eheat_prepare(eheat(matrix(rnorm(81), nrow = 9))) | ||
| #' @keywords internal | ||
| eheat_prepare <- function(object, ...) UseMethod("eheat_prepare") | ||
|
|
||
| #' @export | ||
| #' @rdname eheat_prepare | ||
| eheat_prepare.ExtendedAnnotation <- function(object, ..., | ||
| viewport, heatmap, name) { | ||
| object | ||
| } | ||
| eheat_prepare.default <- function(object, ...) object |
Oops, something went wrong.