| ... | ... |
@@ -159,6 +159,8 @@ export("decorate_row_title")
|
| 159 | 159 |
export("decorate_title")
|
| 160 | 160 |
export("default_axis_param")
|
| 161 | 161 |
export("default_get_type")
|
| 162 |
+export("default_upset_right_annotation")
|
|
| 163 |
+export("default_upset_top_annotation")
|
|
| 162 | 164 |
export("dend_heights")
|
| 163 | 165 |
export("dend_xy")
|
| 164 | 166 |
export("dendrogramGrob")
|
| ... | ... |
@@ -326,6 +326,11 @@ make_comb_mat = function(..., mode = c("distinct", "intersect", "union"),
|
| 326 | 326 |
make_comb_mat_from_list(lt, value_fun, mode = mode, top_n_sets = top_n_sets, min_set_size = min_set_size) |
| 327 | 327 |
} |
| 328 | 328 |
|
| 329 |
+ |
|
| 330 |
+binaryToInt = function(x) {
|
|
| 331 |
+ sum(x * 2^(rev(seq_along(x)) - 1)) |
|
| 332 |
+} |
|
| 333 |
+ |
|
| 329 | 334 |
# == title |
| 330 | 335 |
# Set Names |
| 331 | 336 |
# |
| ... | ... |
@@ -455,9 +460,20 @@ comb_degree = function(m) {
|
| 455 | 460 |
# Extract Elements in a Combination set |
| 456 | 461 |
# |
| 457 | 462 |
# == param |
| 458 |
-# -m |
|
| 459 |
-# -comb_name |
|
| 463 |
+# -m A combination matrix returned by `make_comb_mat`. |
|
| 464 |
+# -comb_name The valid combination set name should be from `comb_name`. |
|
| 465 |
+# |
|
| 466 |
+# == details |
|
| 467 |
+# It returns the combination set. |
|
| 460 | 468 |
# |
| 469 |
+# == example |
|
| 470 |
+# set.seed(123) |
|
| 471 |
+# lt = list(a = sample(letters, 10), |
|
| 472 |
+# b = sample(letters, 15), |
|
| 473 |
+# c = sample(letters, 20)) |
|
| 474 |
+# |
|
| 475 |
+# m = make_comb_mat(lt) |
|
| 476 |
+# extract_comb(m, "110") |
|
| 461 | 477 |
extract_comb = function(m, comb_name) {
|
| 462 | 478 |
all_comb_names = comb_name(m) |
| 463 | 479 |
if(!comb_name %in% all_comb_names) {
|
| ... | ... |
@@ -652,10 +668,75 @@ print.comb_mat = function(x, ...) {
|
| 652 | 668 |
# the position of sets and combination sets. |
| 653 | 669 |
# -set_order The order of sets. |
| 654 | 670 |
# -comb_order The order of combination sets. |
| 671 |
+# -top_annotation A `HeatmapAnnotation` object on top of the combination matrix. |
|
| 672 |
+# -right_annotation A `HeatmapAnnotation` object on the right of the combination matrix. |
|
| 655 | 673 |
# -... Other arguments passed to `Heatmap`. |
| 656 | 674 |
# |
| 675 |
+# == details |
|
| 676 |
+# BY default, the sets are on rows and combination sets are on columns. The positions of the |
|
| 677 |
+# two types of sets can be switched by transposing the matrix. |
|
| 678 |
+# |
|
| 679 |
+# When sets are on rows, the default top annotation is the barplot showing the size of each |
|
| 680 |
+# combination sets and the default right annotation is the barplot showing the size of the sets. |
|
| 681 |
+# The annotations are simply constructed by `HeatmapAnnotation` and `anno_barplot` with some |
|
| 682 |
+# parameters pre-set. Users can check the source code of `default_upset_top_annotation` and |
|
| 683 |
+# `default_upset_right_annotation` to find out how the annotations are defined. |
|
| 684 |
+# |
|
| 685 |
+# To change or to add annotations, users just need to define a new `HeatmapAnnotation` object. |
|
| 686 |
+# E.g. if we want to change the side of the axis and name on top annotation: |
|
| 687 |
+# |
|
| 688 |
+# Upset(..., top_annotation = |
|
| 689 |
+# HeatmapAnnotation( |
|
| 690 |
+# "Intersection size" = anno_barplot( |
|
| 691 |
+# comb_size(m), |
|
| 692 |
+# border = FALSE, |
|
| 693 |
+# gp = gpar(fill = "black"), |
|
| 694 |
+# height = unit(2, "cm"), |
|
| 695 |
+# axis_param = list(side = "right") |
|
| 696 |
+# ), |
|
| 697 |
+# annotation_name_side = "right", |
|
| 698 |
+# annotation_name_rot = 0) |
|
| 699 |
+# ) |
|
| 700 |
+# |
|
| 701 |
+# To add more annotations on top, users just add it in `HeatmapAnnotation`: |
|
| 702 |
+# |
|
| 703 |
+# Upset(..., top_annotation = |
|
| 704 |
+# HeatmapAnnotation( |
|
| 705 |
+# "Intersection size" = anno_barplot( |
|
| 706 |
+# comb_size(m), |
|
| 707 |
+# border = FALSE, |
|
| 708 |
+# gp = gpar(fill = "black"), |
|
| 709 |
+# height = unit(2, "cm"), |
|
| 710 |
+# axis_param = list(side = "right") |
|
| 711 |
+# ), |
|
| 712 |
+# "anno1" = anno_points(...), |
|
| 713 |
+# "anno2" = some_vector, |
|
| 714 |
+# annotation_name_side = "right", |
|
| 715 |
+# annotation_name_rot = 0) |
|
| 716 |
+# ) |
|
| 717 |
+# |
|
| 718 |
+# And so is for the right annotations. |
|
| 719 |
+# |
|
| 720 |
+# `UpSet` returns a `Heatmap-class` object, which means, you can add it with other heatmaps and annotations |
|
| 721 |
+# by ``+`` or `\%v\%`. |
|
| 722 |
+# |
|
| 723 |
+# == example |
|
| 724 |
+# set.seed(123) |
|
| 725 |
+# lt = list(a = sample(letters, 10), |
|
| 726 |
+# b = sample(letters, 15), |
|
| 727 |
+# c = sample(letters, 20)) |
|
| 728 |
+# m = make_comb_mat(lt) |
|
| 729 |
+# UpSet(m) |
|
| 730 |
+# UpSet(t(m)) |
|
| 731 |
+# |
|
| 732 |
+# m = make_comb_mat(lt, mode = "union") |
|
| 733 |
+# UpSet(m) |
|
| 734 |
+# |
|
| 657 | 735 |
UpSet = function(m, set_order = order(set_size(m), decreasing = TRUE), |
| 658 |
- comb_order = order(comb_size(m), decreasing = TRUE), ...) {
|
|
| 736 |
+ comb_order = order(comb_size(m), decreasing = TRUE), |
|
| 737 |
+ top_annotation = default_upset_top_annotation(m), |
|
| 738 |
+ right_annotation = default_upset_right_annotation(m), |
|
| 739 |
+ ...) {
|
|
| 659 | 740 |
|
| 660 | 741 |
set_on_rows = attr(m, "set_on_rows") |
| 661 | 742 |
mode = attr(m, "mode") |
| ... | ... |
@@ -685,11 +766,8 @@ UpSet = function(m, set_order = order(set_size(m), decreasing = TRUE), |
| 685 | 766 |
} |
| 686 | 767 |
ht = Heatmap(m2, cluster_rows = FALSE, cluster_columns = FALSE, rect_gp = gpar(type = "none"), |
| 687 | 768 |
layer_fun = layer_fun, show_heatmap_legend = FALSE, |
| 688 |
- top_annotation = HeatmapAnnotation("Combination size" = anno_barplot(comb_size(m),
|
|
| 689 |
- border = FALSE, gp = gpar(fill = "black"), height = unit(2, "cm")), |
|
| 690 |
- annotation_name_side = "left", annotation_name_rot = 0), |
|
| 691 |
- right_annotation = rowAnnotation("Set size" = anno_barplot(set_size(m), border = FALSE,
|
|
| 692 |
- gp = gpar(fill = "black"), width = unit(3, "cm"))), |
|
| 769 |
+ top_annotation = top_annotation, |
|
| 770 |
+ right_annotation = right_annotation, |
|
| 693 | 771 |
row_names_side = "left", |
| 694 | 772 |
row_order = set_order, column_order = comb_order, ...) |
| 695 | 773 |
} else {
|
| ... | ... |
@@ -713,17 +791,75 @@ UpSet = function(m, set_order = order(set_size(m), decreasing = TRUE), |
| 713 | 791 |
} |
| 714 | 792 |
ht = Heatmap(m2, cluster_rows = FALSE, cluster_columns = FALSE, rect_gp = gpar(type = "none"), |
| 715 | 793 |
layer_fun = layer_fun, show_heatmap_legend = FALSE, |
| 716 |
- right_annotation = rowAnnotation("Combination size" = anno_barplot(comb_size(m),
|
|
| 717 |
- border = FALSE, gp = gpar(fill = "black"), width = unit(2, "cm"))), |
|
| 718 |
- top_annotation = HeatmapAnnotation("Set size" = anno_barplot(set_size(m), border = FALSE, gp = gpar(fill = "black"),
|
|
| 719 |
- height = unit(3, "cm")), |
|
| 720 |
- annotation_name_side = "left", annotation_name_rot = 0), |
|
| 794 |
+ top_annotation = top_annotation, |
|
| 795 |
+ right_annotation = right_annotation, |
|
| 721 | 796 |
row_order = comb_order, column_order = set_order, ...) |
| 722 | 797 |
} |
| 723 | 798 |
ht |
| 724 | 799 |
} |
| 725 | 800 |
|
| 801 |
+# == title |
|
| 802 |
+# Default UpSet Top Annotation |
|
| 803 |
+# |
|
| 804 |
+# == param |
|
| 805 |
+# -m A combination matrix which is as same as the one for `UpSet`. |
|
| 806 |
+# |
|
| 807 |
+# == details |
|
| 808 |
+# The default top annotation is actually barplot implemented by `anno_barplot`. For |
|
| 809 |
+# how to set the top annotation or bottom annotation in `UpSet`, please refer to `UpSet`. |
|
| 810 |
+# |
|
| 811 |
+default_upset_top_annotation = function(m) {
|
|
| 812 |
+ set_on_rows = attr(m, "set_on_rows") |
|
| 813 |
+ |
|
| 814 |
+ if(set_on_rows) {
|
|
| 815 |
+ ha = HeatmapAnnotation("Intersection size" = anno_barplot(comb_size(m),
|
|
| 816 |
+ border = FALSE, gp = gpar(fill = "black"), height = unit(2, "cm")), |
|
| 817 |
+ annotation_name_side = "left", annotation_name_rot = 0) |
|
| 818 |
+ } else {
|
|
| 819 |
+ ha = HeatmapAnnotation("Set size" = anno_barplot(set_size(m), border = FALSE,
|
|
| 820 |
+ gp = gpar(fill = "black"), height = unit(3, "cm")), |
|
| 821 |
+ annotation_name_side = "left", annotation_name_rot = 0) |
|
| 822 |
+ } |
|
| 726 | 823 |
|
| 727 |
-binaryToInt = function(x) {
|
|
| 728 |
- sum(x * 2^(rev(seq_along(x)) - 1)) |
|
| 824 |
+ mode = attr(m, "mode") |
|
| 825 |
+ if(set_on_rows) {
|
|
| 826 |
+ if(mode %in% c("distinct", "intersect")) {
|
|
| 827 |
+ names(ha) = "Intersection size" |
|
| 828 |
+ } else {
|
|
| 829 |
+ names(ha) = "Union size" |
|
| 830 |
+ } |
|
| 831 |
+ } |
|
| 832 |
+ return(ha) |
|
| 833 |
+} |
|
| 834 |
+ |
|
| 835 |
+# == title |
|
| 836 |
+# Default UpSet Right Annotation |
|
| 837 |
+# |
|
| 838 |
+# == param |
|
| 839 |
+# -m A combination matrix which is as same as the one for `UpSet`. |
|
| 840 |
+# |
|
| 841 |
+# == details |
|
| 842 |
+# The default right annotation is actually barplot implemented by `anno_barplot`. For |
|
| 843 |
+# how to set the right annotation or left annotation in `UpSet`, please refer to `UpSet`. |
|
| 844 |
+# |
|
| 845 |
+default_upset_right_annotation = function(m) {
|
|
| 846 |
+ set_on_rows = attr(m, "set_on_rows") |
|
| 847 |
+ |
|
| 848 |
+ if(set_on_rows) {
|
|
| 849 |
+ ha = rowAnnotation("Set size" = anno_barplot(set_size(m), border = FALSE,
|
|
| 850 |
+ gp = gpar(fill = "black"), width = unit(3, "cm"))) |
|
| 851 |
+ } else {
|
|
| 852 |
+ ha = rowAnnotation("Intersection size" = anno_barplot(comb_size(m),
|
|
| 853 |
+ border = FALSE, gp = gpar(fill = "black"), width = unit(2, "cm"))) |
|
| 854 |
+ } |
|
| 855 |
+ |
|
| 856 |
+ mode = attr(m, "mode") |
|
| 857 |
+ if(!set_on_rows) {
|
|
| 858 |
+ if(mode %in% c("distinct", "intersect")) {
|
|
| 859 |
+ names(ha) = "Intersection size" |
|
| 860 |
+ } else {
|
|
| 861 |
+ names(ha) = "Union size" |
|
| 862 |
+ } |
|
| 863 |
+ } |
|
| 864 |
+ return(ha) |
|
| 729 | 865 |
} |
| ... | ... |
@@ -8,18 +8,80 @@ Make the UpSet plot |
| 8 | 8 |
} |
| 9 | 9 |
\usage{
|
| 10 | 10 |
UpSet(m, set_order = order(set_size(m), decreasing = TRUE), |
| 11 |
- comb_order = order(comb_size(m), decreasing = TRUE), ...) |
|
| 11 |
+ comb_order = order(comb_size(m), decreasing = TRUE), |
|
| 12 |
+ top_annotation = default_upset_top_annotation(m), |
|
| 13 |
+ right_annotation = default_upset_right_annotation(m), |
|
| 14 |
+ ...) |
|
| 12 | 15 |
} |
| 13 | 16 |
\arguments{
|
| 14 | 17 |
|
| 15 | 18 |
\item{m}{A combination matrix returned by \code{\link{make_comb_mat}}. The matrix can be transposed to switch the position of sets and combination sets.}
|
| 16 | 19 |
\item{set_order}{The order of sets.}
|
| 17 | 20 |
\item{comb_order}{The order of combination sets.}
|
| 21 |
+ \item{top_annotation}{A \code{\link{HeatmapAnnotation}} object on top of the combination matrix.}
|
|
| 22 |
+ \item{right_annotation}{A \code{\link{HeatmapAnnotation}} object on the right of the combination matrix.}
|
|
| 18 | 23 |
\item{...}{Other arguments passed to \code{\link{Heatmap}}.}
|
| 19 | 24 |
|
| 25 |
+} |
|
| 26 |
+\details{
|
|
| 27 |
+BY default, the sets are on rows and combination sets are on columns. The positions of the |
|
| 28 |
+two types of sets can be switched by transposing the matrix. |
|
| 29 |
+ |
|
| 30 |
+When sets are on rows, the default top annotation is the barplot showing the size of each |
|
| 31 |
+combination sets and the default right annotation is the barplot showing the size of the sets. |
|
| 32 |
+The annotations are simply constructed by \code{\link{HeatmapAnnotation}} and \code{\link{anno_barplot}} with some
|
|
| 33 |
+parameters pre-set. Users can check the source code of \code{\link{default_upset_top_annotation}} and
|
|
| 34 |
+\code{\link{default_upset_right_annotation}} to find out how the annotations are defined.
|
|
| 35 |
+ |
|
| 36 |
+To change or to add annotations, users just need to define a new \code{\link{HeatmapAnnotation}} object.
|
|
| 37 |
+E.g. if we want to change the side of the axis and name on top annotation: |
|
| 38 |
+ |
|
| 39 |
+ \preformatted{
|
|
| 40 |
+ Upset(..., top_annotation = |
|
| 41 |
+ HeatmapAnnotation( |
|
| 42 |
+ "Intersection size" = anno_barplot( |
|
| 43 |
+ comb_size(m), |
|
| 44 |
+ border = FALSE, |
|
| 45 |
+ gp = gpar(fill = "black"), |
|
| 46 |
+ height = unit(2, "cm"), |
|
| 47 |
+ axis_param = list(side = "right") |
|
| 48 |
+ ), |
|
| 49 |
+ annotation_name_side = "right", |
|
| 50 |
+ annotation_name_rot = 0) |
|
| 51 |
+ ) } |
|
| 52 |
+ |
|
| 53 |
+To add more annotations on top, users just add it in \code{\link{HeatmapAnnotation}}:
|
|
| 54 |
+ |
|
| 55 |
+ \preformatted{
|
|
| 56 |
+ Upset(..., top_annotation = |
|
| 57 |
+ HeatmapAnnotation( |
|
| 58 |
+ "Intersection size" = anno_barplot( |
|
| 59 |
+ comb_size(m), |
|
| 60 |
+ border = FALSE, |
|
| 61 |
+ gp = gpar(fill = "black"), |
|
| 62 |
+ height = unit(2, "cm"), |
|
| 63 |
+ axis_param = list(side = "right") |
|
| 64 |
+ ), |
|
| 65 |
+ "anno1" = anno_points(...), |
|
| 66 |
+ "anno2" = some_vector, |
|
| 67 |
+ annotation_name_side = "right", |
|
| 68 |
+ annotation_name_rot = 0) |
|
| 69 |
+ ) } |
|
| 70 |
+ |
|
| 71 |
+And so is for the right annotations. |
|
| 72 |
+ |
|
| 73 |
+\code{\link{UpSet}} returns a \code{\link{Heatmap-class}} object, which means, you can add it with other heatmaps and annotations
|
|
| 74 |
+by \code{+} or \code{\link[=pct_v_pct]{\%v\%}}.
|
|
| 20 | 75 |
} |
| 21 | 76 |
\examples{
|
| 22 |
-# There is no example |
|
| 23 |
-NULL |
|
| 77 |
+set.seed(123) |
|
| 78 |
+lt = list(a = sample(letters, 10), |
|
| 79 |
+ b = sample(letters, 15), |
|
| 80 |
+ c = sample(letters, 20)) |
|
| 81 |
+m = make_comb_mat(lt) |
|
| 82 |
+UpSet(m) |
|
| 83 |
+UpSet(t(m)) |
|
| 24 | 84 |
|
| 85 |
+m = make_comb_mat(lt, mode = "union") |
|
| 86 |
+UpSet(m) |
|
| 25 | 87 |
} |
| 26 | 88 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,25 @@ |
| 1 |
+\name{default_upset_right_annotation}
|
|
| 2 |
+\alias{default_upset_right_annotation}
|
|
| 3 |
+\title{
|
|
| 4 |
+Default UpSet Right Annotation |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Default UpSet Right Annotation |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+default_upset_right_annotation(m) |
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{m}{A combination matrix which is as same as the one for \code{\link{UpSet}}.}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\details{
|
|
| 18 |
+The default right annotation is actually barplot implemented by \code{\link{anno_barplot}}. For
|
|
| 19 |
+how to set the right annotation or left annotation in \code{\link{UpSet}}, please refer to \code{\link{UpSet}}.
|
|
| 20 |
+} |
|
| 21 |
+\examples{
|
|
| 22 |
+# There is no example |
|
| 23 |
+NULL |
|
| 24 |
+ |
|
| 25 |
+} |
| 0 | 26 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,25 @@ |
| 1 |
+\name{default_upset_top_annotation}
|
|
| 2 |
+\alias{default_upset_top_annotation}
|
|
| 3 |
+\title{
|
|
| 4 |
+Default UpSet Top Annotation |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Default UpSet Top Annotation |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+default_upset_top_annotation(m) |
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{m}{A combination matrix which is as same as the one for \code{\link{UpSet}}.}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\details{
|
|
| 18 |
+The default top annotation is actually barplot implemented by \code{\link{anno_barplot}}. For
|
|
| 19 |
+how to set the top annotation or bottom annotation in \code{\link{UpSet}}, please refer to \code{\link{UpSet}}.
|
|
| 20 |
+} |
|
| 21 |
+\examples{
|
|
| 22 |
+# There is no example |
|
| 23 |
+NULL |
|
| 24 |
+ |
|
| 25 |
+} |
| ... | ... |
@@ -11,12 +11,19 @@ extract_comb(m, comb_name) |
| 11 | 11 |
} |
| 12 | 12 |
\arguments{
|
| 13 | 13 |
|
| 14 |
- \item{m}{-m}
|
|
| 15 |
- \item{comb_name}{-comb_name}
|
|
| 14 |
+ \item{m}{A combination matrix returned by \code{\link{make_comb_mat}}.}
|
|
| 15 |
+ \item{comb_name}{The valid combination set name should be from \code{\link{comb_name}}.}
|
|
| 16 | 16 |
|
| 17 |
+} |
|
| 18 |
+\details{
|
|
| 19 |
+It returns the combination set. |
|
| 17 | 20 |
} |
| 18 | 21 |
\examples{
|
| 19 |
-# There is no example |
|
| 20 |
-NULL |
|
| 22 |
+set.seed(123) |
|
| 23 |
+lt = list(a = sample(letters, 10), |
|
| 24 |
+ b = sample(letters, 15), |
|
| 25 |
+ c = sample(letters, 20)) |
|
| 21 | 26 |
|
| 27 |
+m = make_comb_mat(lt) |
|
| 28 |
+extract_comb(m, "110") |
|
| 22 | 29 |
} |
