rename to anno_textbox()

NAMESPACE

@@ -48,8 +48,8 @@ S3method("heightDetails", "legend_body")
 export("heightDetails.legend_body")
 S3method("heightDetails", "packed_legends")
 export("heightDetails.packed_legends")
-S3method("heightDetails", "text_box")
-export("heightDetails.text_box")
+S3method("heightDetails", "textbox")
+export("heightDetails.textbox")
 S3method("length", "HeatmapAnnotation")
 export("length.HeatmapAnnotation")
 S3method("length", "HeatmapList")
@@ -124,8 +124,8 @@ S3method("widthDetails", "legend_body")
 export("widthDetails.legend_body")
 S3method("widthDetails", "packed_legends")
 export("widthDetails.packed_legends")
-S3method("widthDetails", "text_box")
-export("widthDetails.text_box")
+S3method("widthDetails", "textbox")
+export("widthDetails.textbox")
 export("%v%")
 export("AdditiveUnit")
 export("AnnotationFunction")
@@ -159,7 +159,7 @@ export("anno_points")
 export("anno_simple")
 export("anno_summary")
 export("anno_text")
-export("anno_text_box")
+export("anno_textbox")
 export("anno_zoom")
 export("annotation_axis_grob")
 export("bar3D")
@@ -199,7 +199,7 @@ export("getXY_in_parent_vp")
 export("grid.annotation_axis")
 export("grid.boxplot")
 export("grid.dendrogram")
-export("grid.text_box")
+export("grid.textbox")
 export("gt_render")
 export("ht_global_opt")
 export("ht_opt")
@@ -235,7 +235,7 @@ export("subset_matrix_by_row")
 export("subset_no")
 export("subset_vector")
 export("test_alter_fun")
-export("text_box_grob")
+export("textbox_grob")
 export("unify_mat_list")
 export("upset_left_annotation")
 export("upset_right_annotation")
@@ -290,14 +290,14 @@ exportMethods("set_component_height")
 exportMethods("set_component_width")
 
 import(digest)
-import(parallel)
 import(doParallel)
 import(foreach)
 import(grDevices)
 import(graphics)
 import(grid)
 import(matrixStats)
 import(methods)
+import(parallel)
 import(png)
 import(stats)
 importFrom("GetoptLong", qq)
@@ -324,5 +324,4 @@ importFrom("utils", "combn")
 importFrom("utils", "getFromNamespace")
 importFrom("utils", "packageDescription")
 importFrom("utils", "str")
-importFrom("utils", "sessionInfo")
 

R/00_S4_generic_methods.R

@@ -1,32 +1,32 @@
-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
-setGeneric('draw', function(object, ...) standardGeneric('draw'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
 setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
 setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
+setGeneric('draw', function(object, ...) standardGeneric('draw'))
 setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
 setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
 setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
 setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
 setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
 setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

R/HeatmapList-class.R

@@ -410,6 +410,7 @@ setMethod(f = "draw",
     show_parent_dend_line = NULL
     ) {
 
+    .ENV$IS_UNDER_JUPYTER = is_under_jupyter()
 
     if(.ENV$IS_UNDER_JUPYTER && !.ENV$IS_UNDER_JUPYTER_IGNORE) {
         .ENV$IS_UNDER_JUPYTER_IGNORE = TRUE

R/anno_text_box.R → R/anno_textbox.R

@@ -28,15 +28,15 @@
 # == example
 # words = sapply(1:30, function(x) strrep(sample(letters, 1), sample(3:10, 1)))
 # grid.newpage()
-# grid.text_box(words, gp = gpar(fontsize = runif(30, min = 5, max = 30)))
+# grid.textbox(words, gp = gpar(fontsize = runif(30, min = 5, max = 30)))
 #
 # sentenses = c("This is sentense 1", "This is a long long long long long long long sentense.")
 # grid.newpage()
-# grid.text_box(sentenses)
-# grid.text_box(sentenses, word_wrap = TRUE)
-# grid.text_box(sentenses, word_wrap = TRUE, add_new_line = TRUE)
+# grid.textbox(sentenses)
+# grid.textbox(sentenses, word_wrap = TRUE)
+# grid.textbox(sentenses, word_wrap = TRUE, add_new_line = TRUE)
 #
-text_box_grob = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre", 
+textbox_grob = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre", 
 	gp = gpar(), background_gp = gpar(col = "black", fill = "transparent"), round_corners = FALSE, r = unit(0.1, "snpc"),
 	line_space = unit(4, "pt"), text_space = unit(4, "pt"), max_width = unit(100, "mm"), 
 	padding = unit(4, "pt"), first_text_from = "top", add_new_line = FALSE, word_wrap = FALSE) { # width in mm
@@ -203,33 +203,33 @@ text_box_grob = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just
 		# rectGrob(x = x, y = y, width = text_width, height = text_height, default.units = "mm", just = c(0, 0))
 	)
 
-	gb = gTree(children = gl, cl = "text_box", 
+	gb = gTree(children = gl, cl = "textbox", 
 		vp = viewport(x = vp_x, y = vp_y, just = vp_just, width = unit(w, "mm"), 
 			          height = unit(h, "mm")))
 	return(gb)
 }
 
 # == title
-# Width for text_box grob
+# Width for textbox grob
 #
 # == param
-# -x The ``text_box`` grob returned by `text_box_grob`.
+# -x The ``textbox`` grob returned by `textbox_grob`.
 #
 # == value
 # A `grid::unit` object.
-widthDetails.text_box = function(x) {
+widthDetails.textbox = function(x) {
 	x$vp$width
 }
 
 # == title
-# Height for text_box grob
+# Height for textbox grob
 #
 # == param
-# -x The ``text_box`` grob returned by `text_box_grob`.
+# -x The ``textbox`` grob returned by `textbox_grob`.
 #
 # == value
 # A `grid::unit` object.
-heightDetails.text_box = function(x) {
+heightDetails.textbox = function(x) {
 	x$vp$height
 }
 
@@ -241,13 +241,13 @@ heightDetails.text_box = function(x) {
 # -x X position.
 # -y Y position.
 # -gp Graphics parameters of texts.
-# -... Pass to `text_box_grob`.
+# -... Pass to `textbox_grob`.
 #
 # == details
-# All details can be found in the help page of `text_box_grob`.
+# All details can be found in the help page of `textbox_grob`.
 #
-grid.text_box = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp = gpar(), ...) {
-	gb = text_box_grob(text, x = x, y = y, gp = gp, ...)
+grid.textbox = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp = gpar(), ...) {
+	gb = textbox_grob(text, x = x, y = y, gp = gp, ...)
 	grid.draw(gb)
 }
 
@@ -257,15 +257,15 @@ grid.text_box = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp =
 #
 # == param
 # -align_to It controls how the text boxes are aligned to the heatmap rows. The value can be a categorical vector which have the same
-#      length as heatmap rows, or a list of row indices.
+#      length as heatmap rows, or a list of row indices. It does not necessarily include all row indices.
 # -text The corresponding texts. The value should be a list of texts. To control graphics parameters of texts in the boxes, The value
 #    of ``text`` can also be set as a list of data frames where the first column contains the text, from the second column contains
 #    graphics parameters for each text. The column names should be "col", "fontsize", "fontfamily" and "fontface".
 # -background_gp Graphics for the background.
 # -which Only "row" is allowed.
 # -by Are text boxed arranged by `anno_link` or by `anno_block`?
 # -side Side of the annotation to the heatmap.
-# -... Pass to `text_box_grob`.
+# -... Pass to `textbox_grob`.
 #
 # == example
 # require(circlize)
@@ -278,9 +278,9 @@ grid.text_box = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp =
 # names(text) = unique(split)
 #
 # Heatmap(mat, cluster_rows = FALSE, row_split = split,
-#     right_annotation = rowAnnotation(wc = anno_text_box(split, text))
+#     right_annotation = rowAnnotation(wc = anno_textbox(split, text))
 # )
-anno_text_box = function(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"),
+anno_textbox = function(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"),
 	which = c("row", "column"), by = "anno_link", side = c("right", "left"), ...) {
 
 	if(is.null(background_gp$fill)) background_gp$fill = "#DDDDDD"
@@ -290,7 +290,7 @@ anno_text_box = function(align_to, text, background_gp = gpar(fill = "#DDDDDD",
 
 	which = match.arg(which)[1]
 	if(which == "column") {
-		stop_wrap("`anno_text_box()` can only be used as row annotation.")
+		stop_wrap("`anno_textbox()` can only be used as row annotation.")
 	}
 
 	# 1. align_to numeric index, text: a data frame
@@ -328,12 +328,12 @@ anno_text_box = function(align_to, text, background_gp = gpar(fill = "#DDDDDD",
 		stop_wrap("Format of `align_to` or `text` is wrong.")
 	}
 
-	# a list of text_box grobs
+	# a list of textbox grobs
 	dev.null()
 
 	gbl = lapply(text, function(x) {
 		if(is.atomic(x)) {
-			text_box_grob(text = x, background_gp = gpar(col = NA, fill = "transparent"), ...)
+			textbox_grob(text = x, background_gp = gpar(col = NA, fill = "transparent"), ...)
 		} else if(is.data.frame(x)) {
 			if("col" %in% colnames(x)) {
 				col = x$col
@@ -358,7 +358,7 @@ anno_text_box = function(align_to, text, background_gp = gpar(fill = "#DDDDDD",
 			} else {
 				fontface = get.gpar("fontface")[[1]]
 			}
-			text_box_grob(text = x[[1]], gp = gpar(col = col, fontsize = fontsize, fontfamily = fontfamily, fontface = fontface), 
+			textbox_grob(text = x[[1]], gp = gpar(col = col, fontsize = fontsize, fontfamily = fontfamily, fontface = fontface), 
 				background_gp = gpar(col = NA, fill = "transparent"), ...)
 		}
 	})

R/global.R

@@ -247,8 +247,7 @@ GLOBAL_PADDING = unit(rep(5.5, 4), "points")
 
 
 is_under_jupyter = function() {
-    s = sessionInfo()
-    "IRkernel" %in% c(names(s$otherPkgs), names(s$loadedOnly))
+    "IRkernel" %in% loadedNamespaces()
 }
 
 .ENV$IS_UNDER_JUPYTER = FALSE

R/zzz.R

@@ -29,9 +29,6 @@ This message can be suppressed by:
 
     packageStartupMessage(msg)
 
-
-    .ENV$IS_UNDER_JUPYTER = is_under_jupyter()
-    .ENV$IS_UNDER_JUPYTER_IGNORE = FALSE
 }
 
 rv = R.Version()

man/AdditiveUnit-class.Rd

@@ -15,5 +15,4 @@ method and the \code{\%v\%v} method so that above three classes can be appended
 \examples{
 # There is no example
 NULL
-
 }

man/AdditiveUnit.Rd

@@ -26,5 +26,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/AnnotationFunction-class.Rd

@@ -22,5 +22,4 @@ See \code{\link{AnnotationFunction}} constructor for details.
 \examples{
 # There is no example
 NULL
-
 }

man/ColorMapping-class.Rd

@@ -26,5 +26,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/ComplexHeatmap-package.Rd

@@ -40,5 +40,4 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok
 \examples{
 # There is no example
 NULL
-
 }

man/Extract.gridtext.Rd

@@ -22,5 +22,4 @@ Internally used.
 \examples{
 # There is no example
 NULL
-
 }

man/Heatmap-class.Rd

@@ -30,5 +30,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/Heatmap.Rd

@@ -181,8 +181,8 @@ Heatmap(matrix, col, name,
   \item{raster_quality}{A value larger than 1.}
   \item{raster_device_param}{A list of further parameters for the selected graphic device. For raster image support, please check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image} .}
   \item{raster_resize_mat}{Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image? The value can be logical. If it is \code{TRUE}, \code{\link[base]{mean}} is used to summarize the sub matrix which corresponds to a single pixel. The value can also be a summary function, e.g. \code{\link[base:Extremes]{max}}.}
-  \item{raster_by_magick}{Whether to use \code{\link[magick:transform]{image_resize}} to scale the image.}
-  \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick:transform]{image_resize}}. A character scalar and all possible values are in \code{\link[magick:options]{filter_types}}. The default is \code{"Lanczos"}.}
+  \item{raster_by_magick}{Whether to use \code{\link[magick]{image_resize}} to scale the image.}
+  \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick]{image_resize}}. A character scalar and all possible values are in \code{\link[magick]{filter_types}}. The default is \code{"Lanczos"}.}
   \item{post_fun}{A function which will be executed after the heatmap list is drawn.}
 
 }
@@ -212,5 +212,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/HeatmapAnnotation-class.Rd

@@ -25,5 +25,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/HeatmapAnnotation.Rd

@@ -84,5 +84,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/HeatmapList-class.Rd

@@ -27,5 +27,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/HeatmapList.Rd

@@ -26,5 +26,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/Legends.Rd

@@ -26,5 +26,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/SingleAnnotation-class.Rd

@@ -28,5 +28,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }

man/add.AdditiveUnit.Rd

@@ -40,5 +40,4 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
-
 }