Zuguang Gu authored on 20/09/2018 22:09:48 | ... | ... |
@@ -28,6 +28,14 @@ S3method("height<-", "HeatmapAnnotation")
|
| 28 | 28 |
export("height<-.HeatmapAnnotation")
|
| 29 | 29 |
S3method("height<-", "SingleAnnotation")
|
| 30 | 30 |
export("height<-.SingleAnnotation")
|
| 31 |
+S3method("heightDetails", "annotation_axis")
|
|
| 32 |
+export("heightDetails.annotation_axis")
|
|
| 33 |
+S3method("heightDetails", "legend")
|
|
| 34 |
+export("heightDetails.legend")
|
|
| 35 |
+S3method("heightDetails", "legend_body")
|
|
| 36 |
+export("heightDetails.legend_body")
|
|
| 37 |
+S3method("heightDetails", "packed_legends")
|
|
| 38 |
+export("heightDetails.packed_legends")
|
|
| 31 | 39 |
S3method("length", "HeatmapAnnotation")
|
| 32 | 40 |
export("length.HeatmapAnnotation")
|
| 33 | 41 |
S3method("merge", "dendrogram")
|
| ... | ... |
@@ -74,6 +82,14 @@ S3method("width<-", "HeatmapAnnotation")
|
| 74 | 82 |
export("width<-.HeatmapAnnotation")
|
| 75 | 83 |
S3method("width<-", "SingleAnnotation")
|
| 76 | 84 |
export("width<-.SingleAnnotation")
|
| 85 |
+S3method("widthDetails", "annotation_axis")
|
|
| 86 |
+export("widthDetails.annotation_axis")
|
|
| 87 |
+S3method("widthDetails", "legend")
|
|
| 88 |
+export("widthDetails.legend")
|
|
| 89 |
+S3method("widthDetails", "legend_body")
|
|
| 90 |
+export("widthDetails.legend_body")
|
|
| 91 |
+S3method("widthDetails", "packed_legends")
|
|
| 92 |
+export("widthDetails.packed_legends")
|
|
| 77 | 93 |
export("%v%")
|
| 78 | 94 |
export("AdditiveUnit")
|
| 79 | 95 |
export("AnnotationFunction")
|
| ... | ... |
@@ -373,7 +373,6 @@ size.HeatmapAnnotation = function(x, ...) {
|
| 373 | 373 |
} |
| 374 | 374 |
|
| 375 | 375 |
|
| 376 |
- |
|
| 377 | 376 |
# == title |
| 378 | 377 |
# Width of the Legends |
| 379 | 378 |
# |
| ... | ... |
@@ -385,9 +384,11 @@ size.HeatmapAnnotation = function(x, ...) {
|
| 385 | 384 |
# The returned unit x is in ``mm``. |
| 386 | 385 |
# |
| 387 | 386 |
width.Legends = function(x, ...) {
|
| 388 |
- attr(x@grob, "width") |
|
| 387 |
+ s = attr(x@grob, "width") |
|
| 388 |
+ s |
|
| 389 | 389 |
} |
| 390 | 390 |
|
| 391 |
+ |
|
| 391 | 392 |
# == title |
| 392 | 393 |
# Height of the Legends |
| 393 | 394 |
# |
| ... | ... |
@@ -399,6 +400,7 @@ width.Legends = function(x, ...) {
|
| 399 | 400 |
# The returned unit x is in ``mm``. |
| 400 | 401 |
# |
| 401 | 402 |
height.Legends = function(x, ...) {
|
| 402 |
- attr(x@grob, "height") |
|
| 403 |
+ s = attr(x@grob, "height") |
|
| 404 |
+ s |
|
| 403 | 405 |
} |
| 404 | 406 |
|
| ... | ... |
@@ -2607,3 +2607,24 @@ row_anno_link = function(...) {
|
| 2607 | 2607 |
anno_link(..., which = "row") |
| 2608 | 2608 |
} |
| 2609 | 2609 |
|
| 2610 |
+anno_summarize = function(which = c("column", "row"),
|
|
| 2611 |
+ width = NULL, height = NULL, border = FALSE, ...) {
|
|
| 2612 |
+ |
|
| 2613 |
+ if(is.null(.ENV$current_annotation_which)) {
|
|
| 2614 |
+ which = match.arg(which)[1] |
|
| 2615 |
+ } else {
|
|
| 2616 |
+ which = .ENV$current_annotation_which |
|
| 2617 |
+ } |
|
| 2618 |
+ |
|
| 2619 |
+ if(which == "column") {
|
|
| 2620 |
+ stop("`anno_summarize()` is only allowed as a column annotation.")
|
|
| 2621 |
+ } |
|
| 2622 |
+ |
|
| 2623 |
+ anno_size = anno_width_and_height(which, width, height, unit(2, "cm")) |
|
| 2624 |
+ |
|
| 2625 |
+ # get variables fron oncoPrint() function |
|
| 2626 |
+ pf = parent.frame() |
|
| 2627 |
+ # find where the heatmap object is. |
|
| 2628 |
+ |
|
| 2629 |
+} |
|
| 2630 |
+ |
| ... | ... |
@@ -123,7 +123,7 @@ HeatmapAnnotation = function(..., |
| 123 | 123 |
sc = sys.calls() |
| 124 | 124 |
for(i in seq_along(sc)) {
|
| 125 | 125 |
scl = as.list(sc[[i]]) |
| 126 |
- if(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation")) {
|
|
| 126 |
+ if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) {
|
|
| 127 | 127 |
arg_list = scl[-1] |
| 128 | 128 |
break |
| 129 | 129 |
} |
| ... | ... |
@@ -309,7 +309,7 @@ HeatmapAnnotation = function(..., |
| 309 | 309 |
if(!missing(col)) {
|
| 310 | 310 |
unused_col_name = setdiff(names(col), col_name_defined) |
| 311 | 311 |
if(length(unused_col_name)) {
|
| 312 |
- warning(paste0("Following are defined in `col` while have no corresponding annotations:\n", paste(unused_col_name, collapse = ", ")))
|
|
| 312 |
+ # warning(paste0("Following are defined in `col` while have no corresponding annotations:\n", paste(unused_col_name, collapse = ", ")))
|
|
| 313 | 313 |
} |
| 314 | 314 |
} |
| 315 | 315 |
|
| ... | ... |
@@ -120,10 +120,23 @@ annotation_axis_grob = function(at = NULL, labels = at, labels_rot = 0, gp = gpa |
| 120 | 120 |
return(gb) |
| 121 | 121 |
} |
| 122 | 122 |
|
| 123 |
+ |
|
| 124 |
+# == title |
|
| 125 |
+# Grob width for annotation_axis |
|
| 126 |
+# |
|
| 127 |
+# == param |
|
| 128 |
+# -x legend body |
|
| 129 |
+# |
|
| 123 | 130 |
widthDetails.annotation_axis = function(x) {
|
| 124 | 131 |
attr(x, "width") |
| 125 | 132 |
} |
| 126 | 133 |
|
| 134 |
+# == title |
|
| 135 |
+# Grob width for annotation_axis |
|
| 136 |
+# |
|
| 137 |
+# == param |
|
| 138 |
+# -x legend body |
|
| 139 |
+# |
|
| 127 | 140 |
heightDetails.annotation_axis = function(x) {
|
| 128 | 141 |
attr(x, "height") |
| 129 | 142 |
} |
| ... | ... |
@@ -4,7 +4,6 @@ |
| 4 | 4 |
# |
| 5 | 5 |
# == details |
| 6 | 6 |
# This is a very simple class for legends that it only has one slot which is the real `grid::grob` of the legends. |
| 7 |
-# The design of the ``Legends`` class is to support more helper functions such as `width.Legends` to get |
|
| 8 | 7 |
# more information of the legends grob. |
| 9 | 8 |
# |
| 10 | 9 |
# == example |
| ... | ... |
@@ -218,7 +217,7 @@ Legend = function(at, labels = at, col_fun, nrow = NULL, ncol = 1, by_row = FALS |
| 218 | 217 |
textGrob(title, x = title_x, y = unit(1, "npc"), just = title_just, gp = title_gp), |
| 219 | 218 |
edit_vp_in_legend_grob(legend_body, x = unit(0, "npc"), y = unit(0, "npc"), valid.just = c(0, 0)), |
| 220 | 219 |
vp = viewport(width = total_width, height = total_height), |
| 221 |
- cl = "Legend" |
|
| 220 |
+ cl = "legend" |
|
| 222 | 221 |
) |
| 223 | 222 |
attr(gf, "width") = total_width |
| 224 | 223 |
attr(gf, "height") = total_height |
| ... | ... |
@@ -273,7 +272,7 @@ Legend = function(at, labels = at, col_fun, nrow = NULL, ncol = 1, by_row = FALS |
| 273 | 272 |
edit_vp_in_legend_grob(legend_body, x = unit(1, "npc"), y = unit(1, "npc"), |
| 274 | 273 |
valid.just = c(1, 1)), |
| 275 | 274 |
vp = viewport(width = total_width, height = total_height), |
| 276 |
- cl = "Legend" |
|
| 275 |
+ cl = "legend" |
|
| 277 | 276 |
) |
| 278 | 277 |
attr(gf, "width") = total_width |
| 279 | 278 |
attr(gf, "height") = total_height |
| ... | ... |
@@ -761,6 +760,10 @@ packLegend = function(..., gap = unit(2, "mm"), direction = c("vertical", "horiz
|
| 761 | 760 |
} else {
|
| 762 | 761 |
legend_list = list(...) |
| 763 | 762 |
} |
| 763 |
+ if(length(legend_list) == 1) {
|
|
| 764 |
+ return(legend_list[[1]]) |
|
| 765 |
+ } |
|
| 766 |
+ |
|
| 764 | 767 |
legend_list = lapply(legend_list, function(x) {
|
| 765 | 768 |
lgd = x@grob |
| 766 | 769 |
lgd$name = legend_grob_name() |
| ... | ... |
@@ -809,7 +812,6 @@ packLegend = function(..., gap = unit(2, "mm"), direction = c("vertical", "horiz
|
| 809 | 812 |
|
| 810 | 813 |
## pack_width is the width for each column |
| 811 | 814 |
## pack_height is the total height of the packed legends |
| 812 |
- |
|
| 813 | 815 |
gl = list() |
| 814 | 816 |
for(i in 1:nc) {
|
| 815 | 817 |
ind = ind_list[[i]] |
| ... | ... |
@@ -1036,22 +1038,67 @@ grid.draw.Legends = function(x, recording = TRUE) {
|
| 1036 | 1038 |
grid.draw(x@grob, recording = recording) |
| 1037 | 1039 |
} |
| 1038 | 1040 |
|
| 1041 |
+# == title |
|
| 1042 |
+# Grob width for legend_body |
|
| 1043 |
+# |
|
| 1044 |
+# == param |
|
| 1045 |
+# -x legend body |
|
| 1046 |
+# |
|
| 1039 | 1047 |
widthDetails.legend_body = function(x) {
|
| 1040 | 1048 |
attr(x, "width") |
| 1041 | 1049 |
} |
| 1042 | 1050 |
|
| 1051 |
+# == title |
|
| 1052 |
+# Grob height for legend_body |
|
| 1053 |
+# |
|
| 1054 |
+# == param |
|
| 1055 |
+# -x legend body |
|
| 1056 |
+# |
|
| 1043 | 1057 |
heightDetails.legend_body = function(x) {
|
| 1044 | 1058 |
attr(x, "height") |
| 1045 | 1059 |
} |
| 1046 | 1060 |
|
| 1061 |
+# == title |
|
| 1062 |
+# Grob width for packed_legends |
|
| 1063 |
+# |
|
| 1064 |
+# == param |
|
| 1065 |
+# -x legend body |
|
| 1066 |
+# |
|
| 1067 |
+widthDetails.legend = function(x) {
|
|
| 1068 |
+ attr(x, "width") |
|
| 1069 |
+} |
|
| 1070 |
+ |
|
| 1071 |
+# == title |
|
| 1072 |
+# Grob height for packed_legends |
|
| 1073 |
+# |
|
| 1074 |
+# == param |
|
| 1075 |
+# -x legend body |
|
| 1076 |
+# |
|
| 1077 |
+heightDetails.legend = function(x) {
|
|
| 1078 |
+ attr(x, "height") |
|
| 1079 |
+} |
|
| 1080 |
+ |
|
| 1081 |
+# == title |
|
| 1082 |
+# Grob width for packed_legends |
|
| 1083 |
+# |
|
| 1084 |
+# == param |
|
| 1085 |
+# -x legend body |
|
| 1086 |
+# |
|
| 1047 | 1087 |
widthDetails.packed_legends = function(x) {
|
| 1048 | 1088 |
attr(x, "width") |
| 1049 | 1089 |
} |
| 1050 | 1090 |
|
| 1091 |
+# == title |
|
| 1092 |
+# Grob height for packed_legends |
|
| 1093 |
+# |
|
| 1094 |
+# == param |
|
| 1095 |
+# -x legend body |
|
| 1096 |
+# |
|
| 1051 | 1097 |
heightDetails.packed_legends = function(x) {
|
| 1052 | 1098 |
attr(x, "height") |
| 1053 | 1099 |
} |
| 1054 | 1100 |
|
| 1101 |
+ |
|
| 1055 | 1102 |
# assume x is ordered |
| 1056 | 1103 |
is_diff_equal = function(x) {
|
| 1057 | 1104 |
all(abs(diff(diff(x)))/mean(diff(x)) < 1e-4) |
| ... | ... |
@@ -9,7 +9,6 @@ The Class for Legends |
| 9 | 9 |
} |
| 10 | 10 |
\details{
|
| 11 | 11 |
This is a very simple class for legends that it only has one slot which is the real \code{\link[grid]{grob}} of the legends.
|
| 12 |
-The design of the \code{Legends} class is to support more helper functions such as \code{\link{width.Legends}} to get
|
|
| 13 | 12 |
more information of the legends grob. |
| 14 | 13 |
} |
| 15 | 14 |
\examples{
|
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{+.AdditiveUnit}
|
| 2 | 2 |
\alias{+.AdditiveUnit}
|
| 3 |
+\alias{add.AdditiveUnit}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Horizontally Add Heatmaps or Annotations to a Heatmap List |
| 5 | 6 |
} |
| ... | ... |
@@ -25,7 +26,7 @@ The \code{\link{HeatmapAnnotation-class}} object to be added should only be row
|
| 25 | 26 |
A \code{\link{HeatmapList-class}} object.
|
| 26 | 27 |
} |
| 27 | 28 |
\seealso{
|
| 28 |
-\code{\link{\%v\%}} operator is used for vertical heatmap list.
|
|
| 29 |
+\code{\link[=pct_v_pct]{\%v\%}} operator is used for vertical heatmap list.
|
|
| 29 | 30 |
} |
| 30 | 31 |
\author{
|
| 31 | 32 |
Zuguang Gu <z.gu@dkfz.de> |
| ... | ... |
@@ -33,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de> |
| 33 | 34 |
\examples{
|
| 34 | 35 |
# There is no example |
| 35 | 36 |
NULL |
| 37 |
+ |
|
| 36 | 38 |
} |
| ... | ... |
@@ -17,7 +17,7 @@ Add row annotations or heatmaps as a heatmap list |
| 17 | 17 |
|
| 18 | 18 |
} |
| 19 | 19 |
\details{
|
| 20 |
-There is a helper function \code{+.AdditiveUnit} for horizontal add or \code{\link{\%v\%}} for vertical add.
|
|
| 20 |
+There is a helper function \code{+.AdditiveUnit} for horizontal add or \code{\link[=pct_v_pct]{\%v\%}} for vertical add.
|
|
| 21 | 21 |
} |
| 22 | 22 |
\value{
|
| 23 | 23 |
A \code{\link{HeatmapList-class}} object.
|
| ... | ... |
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de> |
| 28 | 28 |
\examples{
|
| 29 | 29 |
# There is no example |
| 30 | 30 |
NULL |
| 31 |
+ |
|
| 31 | 32 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{adjust_heatmap_list-HeatmapList-method}
|
| 2 | 2 |
\alias{adjust_heatmap_list,HeatmapList-method}
|
| 3 |
+\alias{adjust_heatmap_list}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Adjust heatmap list |
| 5 | 6 |
} |
| ... | ... |
@@ -14,8 +15,8 @@ Adjust heatmap list |
| 14 | 15 |
\item{object}{A \code{\link{HeatmapList-class}} object}
|
| 15 | 16 |
|
| 16 | 17 |
} |
| 17 |
-\alias{adjust_heatmap_list}
|
|
| 18 | 18 |
\examples{
|
| 19 | 19 |
# There is no example |
| 20 | 20 |
NULL |
| 21 |
+ |
|
| 21 | 22 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{annotation_legend_size-HeatmapList-method}
|
| 2 | 2 |
\alias{annotation_legend_size,HeatmapList-method}
|
| 3 |
+\alias{annotation_legend_size}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Size of the annotation legend viewport |
| 5 | 6 |
} |
| ... | ... |
@@ -28,8 +29,8 @@ A \code{\link[grid]{unit}} object.
|
| 28 | 29 |
\author{
|
| 29 | 30 |
Zuguang Gu <z.gu@dkfz.de> |
| 30 | 31 |
} |
| 31 |
-\alias{annotation_legend_size}
|
|
| 32 | 32 |
\examples{
|
| 33 | 33 |
# There is no example |
| 34 | 34 |
NULL |
| 35 |
+ |
|
| 35 | 36 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{color_mapping_legend-ColorMapping-method}
|
| 2 | 2 |
\alias{color_mapping_legend,ColorMapping-method}
|
| 3 |
+\alias{color_mapping_legend}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Draw Legend Based on Color Mapping |
| 5 | 6 |
} |
| ... | ... |
@@ -65,8 +66,8 @@ A \code{\link{Legends-class}} object.
|
| 65 | 66 |
\author{
|
| 66 | 67 |
Zuguang Gu <z.gu@dkfz.de> |
| 67 | 68 |
} |
| 68 |
-\alias{color_mapping_legend}
|
|
| 69 | 69 |
\examples{
|
| 70 | 70 |
# There is no example |
| 71 | 71 |
NULL |
| 72 |
+ |
|
| 72 | 73 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{draw_annotation-Heatmap-method}
|
| 2 | 2 |
\alias{draw_annotation,Heatmap-method}
|
| 3 |
+\alias{draw_annotation}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Draw Heatmap Annotations on the Heatmap |
| 5 | 6 |
} |
| ... | ... |
@@ -30,8 +31,8 @@ This function returns no value. |
| 30 | 31 |
\author{
|
| 31 | 32 |
Zuguang Gu <z.gu@dkfz.de> |
| 32 | 33 |
} |
| 33 |
-\alias{draw_annotation}
|
|
| 34 | 34 |
\examples{
|
| 35 | 35 |
# There is no example |
| 36 | 36 |
NULL |
| 37 |
+ |
|
| 37 | 38 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{draw_annotation_legend-HeatmapList-method}
|
| 2 | 2 |
\alias{draw_annotation_legend,HeatmapList-method}
|
| 3 |
+\alias{draw_annotation_legend}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Draw legends for all column annotations |
| 5 | 6 |
} |
| ... | ... |
@@ -27,8 +28,8 @@ This function returns no value. |
| 27 | 28 |
\author{
|
| 28 | 29 |
Zuguang Gu <z.gu@dkfz.de> |
| 29 | 30 |
} |
| 30 |
-\alias{draw_annotation_legend}
|
|
| 31 | 31 |
\examples{
|
| 32 | 32 |
# There is no example |
| 33 | 33 |
NULL |
| 34 |
+ |
|
| 34 | 35 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{draw_dend-Heatmap-method}
|
| 2 | 2 |
\alias{draw_dend,Heatmap-method}
|
| 3 |
+\alias{draw_dend}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Draw Heatmap Dendrograms |
| 5 | 6 |
} |
| ... | ... |
@@ -33,8 +34,8 @@ This function returns no value. |
| 33 | 34 |
\author{
|
| 34 | 35 |
Zuguang Gu <z.gu@dkfz.de> |
| 35 | 36 |
} |
| 36 |
-\alias{draw_dend}
|
|
| 37 | 37 |
\examples{
|
| 38 | 38 |
# There is no example |
| 39 | 39 |
NULL |
| 40 |
+ |
|
| 40 | 41 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{draw_dimnames-Heatmap-method}
|
| 2 | 2 |
\alias{draw_dimnames,Heatmap-method}
|
| 3 |
+\alias{draw_dimnames}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Draw row names or column names |
| 5 | 6 |
} |
| ... | ... |
@@ -29,8 +30,8 @@ This function returns no value. |
| 29 | 30 |
\author{
|
| 30 | 31 |
Zuguang Gu <z.gu@dkfz.de> |
| 31 | 32 |
} |
| 32 |
-\alias{draw_dimnames}
|
|
| 33 | 33 |
\examples{
|
| 34 | 34 |
# There is no example |
| 35 | 35 |
NULL |
| 36 |
+ |
|
| 36 | 37 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{draw_heatmap_body-Heatmap-method}
|
| 2 | 2 |
\alias{draw_heatmap_body,Heatmap-method}
|
| 3 |
+\alias{draw_heatmap_body}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Draw the heatmap body |
| 5 | 6 |
} |
| ... | ... |
@@ -28,8 +29,8 @@ This function returns no value. |
| 28 | 29 |
\author{
|
| 29 | 30 |
Zuguang Gu <z.gu@dkfz.de> |
| 30 | 31 |
} |
| 31 |
-\alias{draw_heatmap_body}
|
|
| 32 | 32 |
\examples{
|
| 33 | 33 |
# There is no example |
| 34 | 34 |
NULL |
| 35 |
+ |
|
| 35 | 36 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{draw_heatmap_legend-HeatmapList-method}
|
| 2 | 2 |
\alias{draw_heatmap_legend,HeatmapList-method}
|
| 3 |
+\alias{draw_heatmap_legend}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Draw legends for all heatmaps |
| 5 | 6 |
} |
| ... | ... |
@@ -27,8 +28,8 @@ This function returns no value. |
| 27 | 28 |
\author{
|
| 28 | 29 |
Zuguang Gu <z.gu@dkfz.de> |
| 29 | 30 |
} |
| 30 |
-\alias{draw_heatmap_legend}
|
|
| 31 | 31 |
\examples{
|
| 32 | 32 |
# There is no example |
| 33 | 33 |
NULL |
| 34 |
+ |
|
| 34 | 35 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{draw_heatmap_list-HeatmapList-method}
|
| 2 | 2 |
\alias{draw_heatmap_list,HeatmapList-method}
|
| 3 |
+\alias{draw_heatmap_list}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Draw the list of heatmaps |
| 5 | 6 |
} |
| ... | ... |
@@ -25,8 +26,8 @@ This function returns no value. |
| 25 | 26 |
\author{
|
| 26 | 27 |
Zuguang Gu <z.gu@dkfz.de> |
| 27 | 28 |
} |
| 28 |
-\alias{draw_heatmap_list}
|
|
| 29 | 29 |
\examples{
|
| 30 | 30 |
# There is no example |
| 31 | 31 |
NULL |
| 32 |
+ |
|
| 32 | 33 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{get_color_mapping_list-HeatmapAnnotation-method}
|
| 2 | 2 |
\alias{get_color_mapping_list,HeatmapAnnotation-method}
|
| 3 |
+\alias{get_color_mapping_list}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Get a List of ColorMapping objects |
| 5 | 6 |
} |
| ... | ... |
@@ -25,8 +26,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.
|
| 25 | 26 |
\author{
|
| 26 | 27 |
Zuguang Gu <z.gu@dkfz.de> |
| 27 | 28 |
} |
| 28 |
-\alias{get_color_mapping_list}
|
|
| 29 | 29 |
\examples{
|
| 30 | 30 |
# There is no example |
| 31 | 31 |
NULL |
| 32 |
+ |
|
| 32 | 33 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{get_legend_param_list-HeatmapAnnotation-method}
|
| 2 | 2 |
\alias{get_legend_param_list,HeatmapAnnotation-method}
|
| 3 |
+\alias{get_legend_param_list}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Get a List of Annotation Legend Parameters |
| 5 | 6 |
} |
| ... | ... |
@@ -25,8 +26,8 @@ A list. |
| 25 | 26 |
\author{
|
| 26 | 27 |
Zuguang Gu <z.gu@dkfz.de> |
| 27 | 28 |
} |
| 28 |
-\alias{get_legend_param_list}
|
|
| 29 | 29 |
\examples{
|
| 30 | 30 |
# There is no example |
| 31 | 31 |
NULL |
| 32 |
+ |
|
| 32 | 33 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{heatmap_legend_size-HeatmapList-method}
|
| 2 | 2 |
\alias{heatmap_legend_size,HeatmapList-method}
|
| 3 |
+\alias{heatmap_legend_size}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Size of the heatmap legend viewport |
| 5 | 6 |
} |
| ... | ... |
@@ -25,8 +26,8 @@ A \code{\link[grid]{unit}} object.
|
| 25 | 26 |
\author{
|
| 26 | 27 |
Zuguang Gu <z.gu@dkfz.de> |
| 27 | 28 |
} |
| 28 |
-\alias{heatmap_legend_size}
|
|
| 29 | 29 |
\examples{
|
| 30 | 30 |
# There is no example |
| 31 | 31 |
NULL |
| 32 |
+ |
|
| 32 | 33 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{height<-.AnnotationFunction}
|
| 2 | 2 |
\alias{height<-.AnnotationFunction}
|
| 3 |
+\alias{heightAssign.AnnotationFunction}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Assign the Height to the AnnotationFunction x |
| 5 | 6 |
} |
| ... | ... |
@@ -19,4 +20,5 @@ Assign the Height to the AnnotationFunction x |
| 19 | 20 |
\examples{
|
| 20 | 21 |
# There is no example |
| 21 | 22 |
NULL |
| 23 |
+ |
|
| 22 | 24 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{height<-.HeatmapAnnotation}
|
| 2 | 2 |
\alias{height<-.HeatmapAnnotation}
|
| 3 |
+\alias{heightAssign.HeatmapAnnotation}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Assign the Height to the HeatmapAnnotation x |
| 5 | 6 |
} |
| ... | ... |
@@ -19,4 +20,5 @@ Assign the Height to the HeatmapAnnotation x |
| 19 | 20 |
\examples{
|
| 20 | 21 |
# There is no example |
| 21 | 22 |
NULL |
| 23 |
+ |
|
| 22 | 24 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{height<-.SingleAnnotation}
|
| 2 | 2 |
\alias{height<-.SingleAnnotation}
|
| 3 |
+\alias{heightAssign.SingleAnnotation}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Assign the Height to the SingleAnnotation x |
| 5 | 6 |
} |
| ... | ... |
@@ -19,4 +20,5 @@ Assign the Height to the SingleAnnotation x |
| 19 | 20 |
\examples{
|
| 20 | 21 |
# There is no example |
| 21 | 22 |
NULL |
| 23 |
+ |
|
| 22 | 24 |
} |
| 23 | 25 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,21 @@ |
| 1 |
+\name{heightDetails.legend}
|
|
| 2 |
+\alias{heightDetails.legend}
|
|
| 3 |
+\title{
|
|
| 4 |
+Grob height for packed_legends |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Grob height for packed_legends |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+\method{heightDetails}{legend}(x)
|
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{x}{legend body}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\examples{
|
|
| 18 |
+# There is no example |
|
| 19 |
+NULL |
|
| 20 |
+ |
|
| 21 |
+} |
| 0 | 22 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,21 @@ |
| 1 |
+\name{heightDetails.annotation_axis}
|
|
| 2 |
+\alias{heightDetails.annotation_axis}
|
|
| 3 |
+\title{
|
|
| 4 |
+Grob width for annotation_axis |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Grob width for annotation_axis |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+\method{heightDetails}{annotation_axis}(x)
|
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{x}{legend body}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\examples{
|
|
| 18 |
+# There is no example |
|
| 19 |
+NULL |
|
| 20 |
+ |
|
| 21 |
+} |
| 0 | 22 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,21 @@ |
| 1 |
+\name{heightDetails.legend_body}
|
|
| 2 |
+\alias{heightDetails.legend_body}
|
|
| 3 |
+\title{
|
|
| 4 |
+Grob height for legend_body |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Grob height for legend_body |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+\method{heightDetails}{legend_body}(x)
|
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{x}{legend body}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\examples{
|
|
| 18 |
+# There is no example |
|
| 19 |
+NULL |
|
| 20 |
+ |
|
| 21 |
+} |
| 0 | 22 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,21 @@ |
| 1 |
+\name{heightDetails.packed_legends}
|
|
| 2 |
+\alias{heightDetails.packed_legends}
|
|
| 3 |
+\title{
|
|
| 4 |
+Grob height for packed_legends |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Grob height for packed_legends |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+\method{heightDetails}{packed_legends}(x)
|
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{x}{legend body}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\examples{
|
|
| 18 |
+# There is no example |
|
| 19 |
+NULL |
|
| 20 |
+ |
|
| 21 |
+} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{make_column_cluster-Heatmap-method}
|
| 2 | 2 |
\alias{make_column_cluster,Heatmap-method}
|
| 3 |
+\alias{make_column_cluster}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Make Cluster on Columns |
| 5 | 6 |
} |
| ... | ... |
@@ -27,8 +28,8 @@ A \code{\link{Heatmap-class}} object.
|
| 27 | 28 |
\author{
|
| 28 | 29 |
Zuguang Gu <z.gu@dkfz.de> |
| 29 | 30 |
} |
| 30 |
-\alias{make_column_cluster}
|
|
| 31 | 31 |
\examples{
|
| 32 | 32 |
# There is no example |
| 33 | 33 |
NULL |
| 34 |
+ |
|
| 34 | 35 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{make_row_cluster-Heatmap-method}
|
| 2 | 2 |
\alias{make_row_cluster,Heatmap-method}
|
| 3 |
+\alias{make_row_cluster}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Make Cluster on Rows |
| 5 | 6 |
} |
| ... | ... |
@@ -27,8 +28,8 @@ A \code{\link{Heatmap-class}} object.
|
| 27 | 28 |
\author{
|
| 28 | 29 |
Zuguang Gu <z.gu@dkfz.de> |
| 29 | 30 |
} |
| 30 |
-\alias{make_row_cluster}
|
|
| 31 | 31 |
\examples{
|
| 32 | 32 |
# There is no example |
| 33 | 33 |
NULL |
| 34 |
+ |
|
| 34 | 35 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{map_to_colors-ColorMapping-method}
|
| 2 | 2 |
\alias{map_to_colors,ColorMapping-method}
|
| 3 |
+\alias{map_to_colors}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Map Values to Colors |
| 5 | 6 |
} |
| ... | ... |
@@ -34,4 +35,3 @@ col_fun = colorRamp2(c(0, 1), c("white", "red"))
|
| 34 | 35 |
cm = ColorMapping(col_fun = col_fun) |
| 35 | 36 |
map_to_colors(cm, runif(10)) |
| 36 | 37 |
} |
| 37 |
-\alias{map_to_colors}
|
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{\%v\%}
|
| 2 | 2 |
\alias{\%v\%}
|
| 3 |
+\alias{pct_v_pct}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Vertically Add Heatmaps or Annotations to a Heatmap List |
| 5 | 6 |
} |
| ... | ... |
@@ -25,7 +26,7 @@ The \code{\link{HeatmapAnnotation-class}} object to be added should only be colu
|
| 25 | 26 |
A \code{\link{HeatmapList-class}} object.
|
| 26 | 27 |
} |
| 27 | 28 |
\seealso{
|
| 28 |
-\code{\link{+.AdditiveUnit}} operator is used for vertical heatmap list.
|
|
| 29 |
+\code{\link[=add.AdditiveUnit]{+.AdditiveUnit}} operator is used for vertical heatmap list.
|
|
| 29 | 30 |
} |
| 30 | 31 |
\author{
|
| 31 | 32 |
Zuguang Gu <z.gu@dkfz.de> |
| ... | ... |
@@ -33,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de> |
| 33 | 34 |
\examples{
|
| 34 | 35 |
# There is no example |
| 35 | 36 |
NULL |
| 37 |
+ |
|
| 36 | 38 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{prepare-Heatmap-method}
|
| 2 | 2 |
\alias{prepare,Heatmap-method}
|
| 3 |
+\alias{prepare}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Prepare the Heatmap |
| 5 | 6 |
} |
| ... | ... |
@@ -33,8 +34,8 @@ The \code{\link{Heatmap-class}} object.
|
| 33 | 34 |
\author{
|
| 34 | 35 |
Zuguang Gu <z.gu@dkfz.de> |
| 35 | 36 |
} |
| 36 |
-\alias{prepare}
|
|
| 37 | 37 |
\examples{
|
| 38 | 38 |
# There is no example |
| 39 | 39 |
NULL |
| 40 |
+ |
|
| 40 | 41 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{resize-HeatmapAnnotation-method}
|
| 2 | 2 |
\alias{resize,HeatmapAnnotation-method}
|
| 3 |
+\alias{resize}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Resize the Width or Height of Heatmap Annotations |
| 5 | 6 |
} |
| ... | ... |
@@ -40,8 +41,8 @@ the basic rule is: |
| 40 | 41 |
and \code{anno_simple_row_size} is disabled.
|
| 41 | 42 |
6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change.
|
| 42 | 43 |
} |
| 43 |
-\alias{resize}
|
|
| 44 | 44 |
\examples{
|
| 45 | 45 |
# There is no example |
| 46 | 46 |
NULL |
| 47 |
+ |
|
| 47 | 48 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{set_component_height-Heatmap-method}
|
| 2 | 2 |
\alias{set_component_height,Heatmap-method}
|
| 3 |
+\alias{set_component_height}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Set Height of Heatmap Component |
| 5 | 6 |
} |
| ... | ... |
@@ -29,8 +30,8 @@ The \code{\link{Heatmap-class}} object.
|
| 29 | 30 |
\author{
|
| 30 | 31 |
Zuguang Gu <z.gu@dkfz.de> |
| 31 | 32 |
} |
| 32 |
-\alias{set_component_height}
|
|
| 33 | 33 |
\examples{
|
| 34 | 34 |
# There is no example |
| 35 | 35 |
NULL |
| 36 |
+ |
|
| 36 | 37 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{set_component_width-Heatmap-method}
|
| 2 | 2 |
\alias{set_component_width,Heatmap-method}
|
| 3 |
+\alias{set_component_width}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Set Width of Heatmap Component |
| 5 | 6 |
} |
| ... | ... |
@@ -28,8 +29,8 @@ The \code{\link{Heatmap-class}} object.
|
| 28 | 29 |
\author{
|
| 29 | 30 |
Zuguang Gu <z.gu@dkfz.de> |
| 30 | 31 |
} |
| 31 |
-\alias{set_component_width}
|
|
| 32 | 32 |
\examples{
|
| 33 | 33 |
# There is no example |
| 34 | 34 |
NULL |
| 35 |
+ |
|
| 35 | 36 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{size<-.HeatmapAnnotation}
|
| 2 | 2 |
\alias{size<-.HeatmapAnnotation}
|
| 3 |
+\alias{sizeAssign.HeatmapAnnotation}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Assign the Size to the HeatmapAnnotation x |
| 5 | 6 |
} |
| ... | ... |
@@ -22,4 +23,5 @@ It assigns the width if it is a row annotation and the height if it is a column |
| 22 | 23 |
\examples{
|
| 23 | 24 |
# There is no example |
| 24 | 25 |
NULL |
| 26 |
+ |
|
| 25 | 27 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{size<-.SingleAnnotation}
|
| 2 | 2 |
\alias{size<-.SingleAnnotation}
|
| 3 |
+\alias{sizeAssign.SingleAnnotation}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Assign the Size of the SingleAnnotation x |
| 5 | 6 |
} |
| ... | ... |
@@ -22,4 +23,5 @@ It assigns the width if it is a row annotation and the height if it is a column |
| 22 | 23 |
\examples{
|
| 23 | 24 |
# There is no example |
| 24 | 25 |
NULL |
| 26 |
+ |
|
| 25 | 27 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{width<-.AnnotationFunction}
|
| 2 | 2 |
\alias{width<-.AnnotationFunction}
|
| 3 |
+\alias{widthAssign.AnnotationFunction}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Assign the Width to the AnnotationFunction x |
| 5 | 6 |
} |
| ... | ... |
@@ -19,4 +20,5 @@ Assign the Width to the AnnotationFunction x |
| 19 | 20 |
\examples{
|
| 20 | 21 |
# There is no example |
| 21 | 22 |
NULL |
| 23 |
+ |
|
| 22 | 24 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{width<-.HeatmapAnnotation}
|
| 2 | 2 |
\alias{width<-.HeatmapAnnotation}
|
| 3 |
+\alias{widthAssign.HeatmapAnnotation}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Assign the Width to the HeatmapAnnotation x |
| 5 | 6 |
} |
| ... | ... |
@@ -19,4 +20,5 @@ Assign the Width to the HeatmapAnnotation x |
| 19 | 20 |
\examples{
|
| 20 | 21 |
# There is no example |
| 21 | 22 |
NULL |
| 23 |
+ |
|
| 22 | 24 |
} |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
\name{width<-.SingleAnnotation}
|
| 2 | 2 |
\alias{width<-.SingleAnnotation}
|
| 3 |
+\alias{widthAssign.SingleAnnotation}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Assign the Width to the SingleAnnotation x |
| 5 | 6 |
} |
| ... | ... |
@@ -19,4 +20,5 @@ Assign the Width to the SingleAnnotation x |
| 19 | 20 |
\examples{
|
| 20 | 21 |
# There is no example |
| 21 | 22 |
NULL |
| 23 |
+ |
|
| 22 | 24 |
} |
| 23 | 25 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,21 @@ |
| 1 |
+\name{widthDetails.legend}
|
|
| 2 |
+\alias{widthDetails.legend}
|
|
| 3 |
+\title{
|
|
| 4 |
+Grob width for packed_legends |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Grob width for packed_legends |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+\method{widthDetails}{legend}(x)
|
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{x}{legend body}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\examples{
|
|
| 18 |
+# There is no example |
|
| 19 |
+NULL |
|
| 20 |
+ |
|
| 21 |
+} |
| 0 | 22 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,21 @@ |
| 1 |
+\name{widthDetails.annotation_axis}
|
|
| 2 |
+\alias{widthDetails.annotation_axis}
|
|
| 3 |
+\title{
|
|
| 4 |
+Grob width for annotation_axis |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Grob width for annotation_axis |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+\method{widthDetails}{annotation_axis}(x)
|
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{x}{legend body}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\examples{
|
|
| 18 |
+# There is no example |
|
| 19 |
+NULL |
|
| 20 |
+ |
|
| 21 |
+} |
| 0 | 22 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,21 @@ |
| 1 |
+\name{widthDetails.legend_body}
|
|
| 2 |
+\alias{widthDetails.legend_body}
|
|
| 3 |
+\title{
|
|
| 4 |
+Grob width for legend_body |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Grob width for legend_body |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+\method{widthDetails}{legend_body}(x)
|
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{x}{legend body}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\examples{
|
|
| 18 |
+# There is no example |
|
| 19 |
+NULL |
|
| 20 |
+ |
|
| 21 |
+} |
| 0 | 22 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,21 @@ |
| 1 |
+\name{widthDetails.packed_legends}
|
|
| 2 |
+\alias{widthDetails.packed_legends}
|
|
| 3 |
+\title{
|
|
| 4 |
+Grob width for packed_legends |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+Grob width for packed_legends |
|
| 8 |
+} |
|
| 9 |
+\usage{
|
|
| 10 |
+\method{widthDetails}{packed_legends}(x)
|
|
| 11 |
+} |
|
| 12 |
+\arguments{
|
|
| 13 |
+ |
|
| 14 |
+ \item{x}{legend body}
|
|
| 15 |
+ |
|
| 16 |
+} |
|
| 17 |
+\examples{
|
|
| 18 |
+# There is no example |
|
| 19 |
+NULL |
|
| 20 |
+ |
|
| 21 |
+} |
| 0 | 22 |
new file mode 100755 |
| ... | ... |
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| 1 |
+#toc {
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| 2 |
+ position: fixed; |
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| 3 |
+ left: 0; |
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+ top: 20px; |
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+ width: 200px; |
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+ height: 100%; |
|
| 7 |
+ overflow:auto; |
|
| 8 |
+ padding: 0px 10px 0px 10px; |
|
| 9 |
+} |
|
| 10 |
+#toc_header {
|
|
| 11 |
+ display: none; |
|
| 12 |
+} |
|
| 13 |
+#toc ul {
|
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| 14 |
+ margin: 0px; |
|
| 15 |
+ padding: 0px; |
|
| 16 |
+} |
|
| 17 |
+#toc ul li {
|
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| 18 |
+ list-style-type: none; |
|
| 19 |
+} |
|
| 20 |
+ |
|
| 21 |
+#toc ul li ul li {
|
|
| 22 |
+ margin-left: 15px; |
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+ list-style-type: circle; |
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+} |
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+body, td {
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+ font-family: Arial,Helvetica,sans-serif; |
|
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+ background-color: white; |
|
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+ font-size: 13px; |
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+ max-width: 800px; |
|
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+ margin: auto; |
|
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+ margin-left:210px; |
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+ padding: 0px 10px 0px 10px; |
|
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+ border-left: 1px solid #EEEEEE; |
|
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+ line-height: 150%; |
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+} |
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+ |
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+tt, code, pre {
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+ font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, |
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+ |
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+monospace; |
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+} |
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+ |
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+h1 {
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+ font-size:2.2em; |
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+} |
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+} |
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+ |
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+ font-size:1.4em; |
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+} |
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+ |
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+h4 {
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+ font-size:1.0em; |
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+} |
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+ |
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+h5 {
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+ font-size:0.9em; |
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+} |
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+ |
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+h6 {
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+ font-size:0.8em; |
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+} |
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+ |
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+a {
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+ text-decoration: none; |
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+} |
|
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+ |
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+a:hover {
|
|
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+ text-decoration: underline; |
|
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+} |
|
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+ |
|
| 75 |
+a:visited {
|
|
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+ color: rgb(50%, 0%, 50%); |
|
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+} |
|
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+ |
|
| 79 |
+pre, img {
|
|
| 80 |
+ max-width: 100%; |
|
| 81 |
+} |
|
| 82 |
+pre {
|
|
| 83 |
+ overflow-x: auto; |
|
| 84 |
+} |
|
| 85 |
+pre code {
|
|
| 86 |
+ display: block; padding: 0.5em; |
|
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+} |
|
| 88 |
+ |
|
| 89 |
+code {
|
|
| 90 |
+ font-size: 92%; |
|
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+ border: 1px solid #ccc; |
|
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+} |
|
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+ |
|
| 94 |
+code[class] {
|
|
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+ background-color: #F8F8F8; |
|
| 96 |
+} |
|
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+ |
|
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+table, td, th {
|
|
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+ border: none; |
|
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+} |
|
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+ |
|
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+blockquote {
|
|
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+ color:#666666; |
|
| 104 |
+ margin:0; |
|
| 105 |
+ padding-left: 1em; |
|
| 106 |
+ border-left: 0.5em #EEE solid; |
|
| 107 |
+} |
|
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+ |
|
| 109 |
+hr {
|
|
| 110 |
+ height: 0px; |
|
| 111 |
+ border-bottom: none; |
|
| 112 |
+ border-top-width: thin; |
|
| 113 |
+ border-top-style: dotted; |
|
| 114 |
+ border-top-color: #999999; |
|
| 115 |
+} |
|
| 116 |
+ |
|
| 117 |
+@media print {
|
|
| 118 |
+ * {
|
|
| 119 |
+ background: transparent !important; |
|
| 120 |
+ color: black !important; |
|
| 121 |
+ filter:none !important; |
|
| 122 |
+ -ms-filter: none !important; |
|
| 123 |
+ } |
|
| 124 |
+ |
|
| 125 |
+ body {
|
|
| 126 |
+ font-size:12pt; |
|
| 127 |
+ max-width:100%; |
|
| 128 |
+ } |
|
| 129 |
+ |
|
| 130 |
+ a, a:visited {
|
|
| 131 |
+ text-decoration: underline; |
|
| 132 |
+ } |
|
| 133 |
+ |
|
| 134 |
+ hr {
|
|
| 135 |
+ visibility: hidden; |
|
| 136 |
+ page-break-before: always; |
|
| 137 |
+ } |
|
| 138 |
+ |
|
| 139 |
+ pre, blockquote {
|
|
| 140 |
+ padding-right: 1em; |
|
| 141 |
+ page-break-inside: avoid; |
|
| 142 |
+ } |
|
| 143 |
+ |
|
| 144 |
+ tr, img {
|
|
| 145 |
+ page-break-inside: avoid; |
|
| 146 |
+ } |
|
| 147 |
+ |
|
| 148 |
+ img {
|
|
| 149 |
+ max-width: 100% !important; |
|
| 150 |
+ } |
|
| 151 |
+ |
|
| 152 |
+ @page :left {
|
|
| 153 |
+ margin: 15mm 20mm 15mm 10mm; |
|
| 154 |
+ } |
|
| 155 |
+ |
|
| 156 |
+ @page :right {
|
|
| 157 |
+ margin: 15mm 10mm 15mm 20mm; |
|
| 158 |
+ } |
|
| 159 |
+ |
|
| 160 |
+ p, h2, h3 {
|
|
| 161 |
+ orphans: 3; widows: 3; |
|
| 162 |
+ } |
|
| 163 |
+ |
|
| 164 |
+ h2, h3 {
|
|
| 165 |
+ page-break-after: avoid; |
|
| 166 |
+ } |
|
| 167 |
+} |
| 0 | 168 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,124 @@ |
| 1 |
+ |
|
| 2 |
+set.seed(888) |
|
| 3 |
+ |
|
| 4 |
+type = c(rep("Tumor", 10), rep("Control", 10))
|
|
| 5 |
+gender = sample(c("F", "M"), 20, replace = TRUE)
|
|
| 6 |
+gender[sample(1:20, 2)] = NA |
|
| 7 |
+age = runif(20, min = 30, max = 80) |
|
| 8 |
+mutation = data.frame(mut1 = sample(c(TRUE, FALSE), 20, p = c(0.2, 0.8), replace = TRUE), |
|
| 9 |
+ mut2 = sample(c(TRUE, FALSE), 20, p = c(0.3, 0.7), replace = TRUE)) |
|
| 10 |
+anno = data.frame(type = type, gender = gender, age = age, mutation, stringsAsFactors = FALSE) |
|
| 11 |
+ |
|
| 12 |
+anno_col = list(type = c("Tumor" = "red", "Control" = "blue"),
|
|
| 13 |
+ gender = c("F" = "pink", "M" = "darkgreen"),
|
|
| 14 |
+ mutation = c("TRUE" = "black", "FALSE" = "white"))
|
|
| 15 |
+ |
|
| 16 |
+###################################### |
|
| 17 |
+# generate methylation matrix |
|
| 18 |
+rand_meth = function(k, mean) {
|
|
| 19 |
+ (runif(k) - 0.5)*min(c(1-mean), mean) + mean |
|
| 20 |
+} |
|
| 21 |
+ |
|
| 22 |
+mean_meth = c(rand_meth(300, 0.3), rand_meth(700, 0.7)) |
|
| 23 |
+mat_meth = as.data.frame(lapply(mean_meth, function(m) {
|
|
| 24 |
+ if(m < 0.3) {
|
|
| 25 |
+ c(rand_meth(10, m), rand_meth(10, m + 0.2)) |
|
| 26 |
+ } else if(m > 0.7) {
|
|
| 27 |
+ c(rand_meth(10, m), rand_meth(10, m - 0.2)) |
|
| 28 |
+ } else {
|
|
| 29 |
+ c(rand_meth(10, m), rand_meth(10, m + sample(c(1, -1), 1)*0.2)) |
|
| 30 |
+ } |
|
| 31 |
+ |
|
| 32 |
+})) |
|
| 33 |
+mat_meth = t(mat_meth) |
|
| 34 |
+rownames(mat_meth) = NULL |
|
| 35 |
+colnames(mat_meth) = paste0("sample", 1:20)
|
|
| 36 |
+ |
|
| 37 |
+###################################### |
|
| 38 |
+# generate directions for methylation |
|
| 39 |
+direction = rowMeans(mat_meth[, 1:10]) - rowMeans(mat_meth[, 11:20]) |
|
| 40 |
+direction = ifelse(direction > 0, "hyper", "hypo") |
|
| 41 |
+library(circlize) |
|
| 42 |
+ |
|
| 43 |
+####################################### |
|
| 44 |
+# generate expression matrix |
|
| 45 |
+mat_expr = t(apply(mat_meth, 1, function(x) {
|
|
| 46 |
+ x = x + rnorm(length(x), sd = abs(runif(1)-0.5)*0.4 + 0.1) |
|
| 47 |
+ -scale(x) |
|
| 48 |
+})) |
|
| 49 |
+dimnames(mat_expr) = dimnames(mat_meth) |
|
| 50 |
+ |
|
| 51 |
+############################################################# |
|
| 52 |
+# matrix for correlation between methylation and expression |
|
| 53 |
+cor_pvalue = -log10(sapply(seq_len(nrow(mat_meth)), function(i) {
|
|
| 54 |
+ cor.test(mat_meth[i, ], mat_expr[i, ])$p.value |
|
| 55 |
+})) |
|
| 56 |
+ |
|
| 57 |
+##################################################### |
|
| 58 |
+# matrix for types of genes |
|
| 59 |
+gene_type = sample(c("protein_coding", "lincRNA", "microRNA", "psedo-gene", "others"),
|
|
| 60 |
+ nrow(mat_meth), replace = TRUE, prob = c(6, 1, 1, 1, 1)) |
|
| 61 |
+ |
|
| 62 |
+################################################# |
|
| 63 |
+# annotation to genes |
|
| 64 |
+anno_gene = sapply(mean_meth, function(m) {
|
|
| 65 |
+ if(m > 0.6) {
|
|
| 66 |
+ if(runif(1) < 0.8) return("intragenic")
|
|
| 67 |
+ } |
|
| 68 |
+ if(m < 0.4) {
|
|
| 69 |
+ if(runif(1) < 0.4) return("TSS")
|
|
| 70 |
+ } |
|
| 71 |
+ return("intergenic")
|
|
| 72 |
+}) |
|
| 73 |
+ |
|
| 74 |
+anno_gene_col = c("intragenic" = "blue", "TSS" = "red", "intergenic" = "grey")
|
|
| 75 |
+ |
|
| 76 |
+############################################ |
|
| 77 |
+# distance to genes |
|
| 78 |
+tss_dist = sapply(mean_meth, function(m) {
|
|
| 79 |
+ if(m < 0.3) {
|
|
| 80 |
+ if(runif(1) < 0.5) {
|
|
| 81 |
+ return(round( (runif(1) - 0.5)*1000 + 500)) |
|
| 82 |
+ } else {
|
|
| 83 |
+ return(round( (runif(1) - 0.5)*10000 + 500)) |
|
| 84 |
+ } |
|
| 85 |
+ } else if(m < 0.6) {
|
|
| 86 |
+ if(runif(1) < 0.8) {
|
|
| 87 |
+ return(round( (runif(1)-0.5)*100000 + 50000 )) |
|
| 88 |
+ } else {
|
|
| 89 |
+ return(round( (runif(1)-0.5)*1000000 + 500000 )) |
|
| 90 |
+ } |
|
| 91 |
+ } |
|
| 92 |
+ return(round( (runif(1) - 0.5)*1000000 + 500000)) |
|
| 93 |
+}) |
|
| 94 |
+ |
|
| 95 |
+ |
|
| 96 |
+####################################### |
|
| 97 |
+# annotation to enhancers |
|
| 98 |
+rand_tss = function(m) {
|
|
| 99 |
+ if(m < 0.4) {
|
|
| 100 |
+ if(runif(1) < 0.25) return(runif(1)) |
|
| 101 |
+ } else if (runif(1) < 0.1) {
|
|
| 102 |
+ return(runif(1)) |
|
| 103 |
+ } |
|
| 104 |
+ return(0) |
|
| 105 |
+} |
|
| 106 |
+rand_enhancer = function(m) {
|
|
| 107 |
+ if(m < 0.4) {
|
|
| 108 |
+ if(runif(1) < 0.6) return(runif(1)) |
|
| 109 |
+ } else if (runif(1) < 0.1) {
|
|
| 110 |
+ return(runif(1)) |
|
| 111 |
+ } |
|
| 112 |
+ return(0) |
|
| 113 |
+} |
|
| 114 |
+rand_repressive = function(m) {
|
|
| 115 |
+ if(m > 0.4) {
|
|
| 116 |
+ if(runif(1) < 0.8) return(runif(1)) |
|
| 117 |
+ } |
|
| 118 |
+ return(0) |
|
| 119 |
+} |
|
| 120 |
+anno_states = data.frame( |
|
| 121 |
+ tss = sapply(mean_meth, rand_tss), |
|
| 122 |
+ enhancer = sapply(mean_meth, rand_enhancer), |
|
| 123 |
+ rand_repressive = sapply(mean_meth, rand_repressive)) |
|
| 124 |
+ |
| 0 | 125 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,115 @@ |
| 1 |
+<!-- |
|
| 2 |
+%\VignetteEngine{knitr}
|
|
| 3 |
+%\VignetteIndexEntry{Common use of ComplexHeatmap package}
|
|
| 4 |
+--> |
|
| 5 |
+ |
|
| 6 |
+Common use of ComplexHeatmap package |
|
| 7 |
+======================================== |
|
| 8 |
+ |
|
| 9 |
+**Author**: Zuguang Gu ( z.gu@dkfz.de ) |
|
| 10 |
+ |
|
| 11 |
+**Date**: `r Sys.Date()` |
|
| 12 |
+ |
|
| 13 |
+------------------------------------------------------------- |
|
| 14 |
+ |
|
| 15 |
+```{r global_settings, echo = FALSE, message = FALSE}
|
|
| 16 |
+library(markdown) |
|
| 17 |
+options(markdown.HTML.options = c(options('markdown.HTML.options')[[1]], "toc"))
|
|
| 18 |
+ |
|
| 19 |
+library(knitr) |
|
| 20 |
+knitr::opts_chunk$set( |
|
| 21 |
+ error = FALSE, |
|
| 22 |
+ tidy = FALSE, |
|
| 23 |
+ message = FALSE, |
|
| 24 |
+ fig.align = "center" |
|
| 25 |
+) |
|
| 26 |
+options(markdown.HTML.stylesheet = "custom.css") |
|
| 27 |
+ |
|
| 28 |
+options(width = 100) |
|
| 29 |
+``` |
|
| 30 |
+ |
|
| 31 |
+```{r}
|
|
| 32 |
+library(circlize) |
|
| 33 |
+library(ComplexHeatmap) |
|
| 34 |
+ |
|
| 35 |
+source("generate_random_dataset.R")
|
|
| 36 |
+``` |
|
| 37 |
+ |
|
| 38 |
+# A Single Heatmap with annotations |
|
| 39 |
+ |
|
| 40 |
+```{r}
|
|
| 41 |
+Heatmap(mat_meth, name = "methylation", |
|
| 42 |
+ top_annotation = HeatmapAnnotation( |
|
| 43 |
+ type = anno$type, |
|
| 44 |
+ gender = anno$gender, |
|
| 45 |
+ age = anno_points(anno$age, ylim = c(0, 80)), |
|
| 46 |
+ mutation = as.matrix(anno[, c("mut1", "mut2")]),
|
|
| 47 |
+ col = anno_col |
|
| 48 |
+ ), column_title = "Differential Methylated Regions") |
|
| 49 |
+``` |
|
| 50 |
+ |
|
| 51 |
+```{r}
|
|
| 52 |
+Heatmap(mat_meth, name = "methylation", |
|
| 53 |
+ top_annotation = HeatmapAnnotation( |
|
| 54 |
+ df = anno, |
|
| 55 |
+ annotation_name_side = "left" |
|
| 56 |
+ ), column_title = "Differential Methylated Regions") |
|
| 57 |
+``` |
|
| 58 |
+ |
|
| 59 |
+```{r}
|
|
| 60 |
+Heatmap(mat_meth, name = "methylation", |
|
| 61 |
+ top_annotation = HeatmapAnnotation( |
|
| 62 |
+ df = anno, |
|
| 63 |
+ col = anno_col, |
|
| 64 |
+ annotation_name_side = "left" |
|
| 65 |
+ ), |
|
| 66 |
+ right_annotation = rowAnnotation( |
|
| 67 |
+ anno_gene = anno_gene, |
|
| 68 |
+ tss_dist = anno_points(tss_dist), |
|
| 69 |
+ col = list(anno_gene = anno_gene_col) |
|
| 70 |
+ ), |
|
| 71 |
+ column_title = "Differential Methylated Regions") |
|
| 72 |
+``` |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+```{r}
|
|
| 76 |
+Heatmap(mat_meth, name = "methylation", |
|
| 77 |
+ top_annotation = HeatmapAnnotation( |
|
| 78 |
+ type = anno$type, |
|
| 79 |
+ gender = anno$gender, |
|
| 80 |
+ age = anno_points(anno$age, ylim = c(0, 80)), |
|
| 81 |
+ mutation = as.matrix(anno[, c("mut1", "mut2")]),
|
|
| 82 |
+ col = anno_col |
|
| 83 |
+ ), |
|
| 84 |
+ right_annotation = rowAnnotation( |
|
| 85 |
+ anno_gene = anno_gene, |
|
| 86 |
+ tss_dist = anno_points(tss_dist), |
|
| 87 |
+ col = list(anno_gene = anno_gene_col) |
|
| 88 |
+ ), |
|
| 89 |
+ show_column_names = FALSE, |
|
| 90 |
+ column_title = "Differential Methylated Regions", |
|
| 91 |
+ column_km = 2, row_km = 4) |
|
| 92 |
+``` |
|
| 93 |
+ |
|
| 94 |
+ |
|
| 95 |
+## Heatmap List |
|
| 96 |
+ |
|
| 97 |
+```{r}
|
|
| 98 |
+meth_col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"))
|
|
| 99 |
+expr_col_fun = colorRamp2(c(-2, 0, 2), c("green", "white", "red"))
|
|
| 100 |
+ht_list = Heatmap(mat_meth, name = "methylation", col = meth_col_fun) + |
|
| 101 |
+ Heatmap(mat_expr, name = "epxression", col = expr_col_fun) |
|
| 102 |
+draw(ht_list, row_km = 4) |
|
| 103 |
+``` |
|
| 104 |
+ |
|
| 105 |
+ |
|
| 106 |
+```{r}
|
|
| 107 |
+ht_list = Heatmap(mat_meth[1:40, ], name = "methylation", col = meth_col_fun) %v% |
|
| 108 |
+ Heatmap(mat_expr[1:40, ], name = "epxression", col = expr_col_fun) |
|
| 109 |
+draw(ht_list, column_km = 2) |
|
| 110 |
+``` |
|
| 111 |
+ |
|
| 112 |
+## OncoPrint |
|
| 113 |
+ |
|
| 114 |
+## Density as a heatmap |
|
| 115 |
+ |