Zuguang Gu authored on 28/09/2019 08:37:13 | ... | ... |
@@ -9,6 +9,9 @@ CHANGES in VERSION 2.1.0 |
| 9 | 9 |
* `densityHeatmap()`: `col` can be set as a function |
| 10 | 10 |
* add `cluster_rows`/`cluster_columns` in `oncoPrint()` |
| 11 | 11 |
* legend labels support symbols |
| 12 |
+* `Heatmap()`: add `jitter` argument to add tiny random shift to original matrix. |
|
| 13 |
+ It is mainly to solve the problem of "Error: node stack overflow" |
|
| 14 |
+ when there are too many identical rows/columns for plotting the dendrograms. |
|
| 12 | 15 |
|
| 13 | 16 |
======================== |
| 14 | 17 |
|
| ... | ... |
@@ -93,6 +93,10 @@ Heatmap = setClass("Heatmap",
|
| 93 | 93 |
# row index in ``matrix``, coordinate of the cell, |
| 94 | 94 |
# the width and height of the cell and the filled color. ``x``, ``y``, ``width`` and ``height`` are all `grid::unit` objects. |
| 95 | 95 |
# -layer_fun Similar as ``cell_fun``, but is vectorized. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#customize-the-heatmap-body . |
| 96 |
+# -jitter Random shifts added to the matrix. The value can be logical or a single numeric value. It it is ``TRUE``, random |
|
| 97 |
+# values from uniform distribution between 0 and 1e-10 are generated. If it is a numeric value, |
|
| 98 |
+# the range for the uniform distribution is (0, ``jitter``). It is mainly to solve the problem of "Error: node stack overflow" |
|
| 99 |
+# when there are too many identical rows/columns for plotting the dendrograms. |
|
| 96 | 100 |
# -row_title Title on the row. |
| 97 | 101 |
# -row_title_side Will the title be put on the left or right of the heatmap? |
| 98 | 102 |
# -row_title_gp Graphic parameters for row title. |
| ... | ... |
@@ -206,6 +210,7 @@ Heatmap = function(matrix, col, name, |
| 206 | 210 |
border = NA, |
| 207 | 211 |
cell_fun = NULL, |
| 208 | 212 |
layer_fun = NULL, |
| 213 |
+ jitter = FALSE, |
|
| 209 | 214 |
|
| 210 | 215 |
row_title = character(0), |
| 211 | 216 |
row_title_side = c("left", "right"),
|
| ... | ... |
@@ -437,6 +442,7 @@ Heatmap = function(matrix, col, name, |
| 437 | 442 |
.Object@matrix_param$column_km = column_km |
| 438 | 443 |
.Object@matrix_param$column_km_repeats = column_km_repeats |
| 439 | 444 |
.Object@matrix_param$column_gap = column_gap |
| 445 |
+ .Object@matrix_param$jitter = jitter |
|
| 440 | 446 |
|
| 441 | 447 |
### check row_split and column_split ### |
| 442 | 448 |
if(!is.null(row_split)) {
|
| ... | ... |
@@ -943,6 +949,17 @@ make_cluster = function(object, which = c("row", "column")) {
|
| 943 | 949 |
} |
| 944 | 950 |
|
| 945 | 951 |
mat = object@matrix |
| 952 |
+ jitter = object@matrix_param$jitter |
|
| 953 |
+ if(is.numeric(mat)) {
|
|
| 954 |
+ if(is.logical(jitter)) {
|
|
| 955 |
+ if(jitter) {
|
|
| 956 |
+ mat = mat + runif(length(mat), min = 0, max = 1e-10) |
|
| 957 |
+ } |
|
| 958 |
+ } else {
|
|
| 959 |
+ mat = mat + runif(length(mat), min = 0, max = jitter + 0) |
|
| 960 |
+ } |
|
| 961 |
+ } |
|
| 962 |
+ |
|
| 946 | 963 |
distance = slot(object, paste0(which, "_dend_param"))$distance |
| 947 | 964 |
method = slot(object, paste0(which, "_dend_param"))$method |
| 948 | 965 |
order = slot(object, paste0(which, "_order")) # pre-defined row order |
| ... | ... |
@@ -14,6 +14,7 @@ Heatmap(matrix, col, name, |
| 14 | 14 |
border = NA, |
| 15 | 15 |
cell_fun = NULL, |
| 16 | 16 |
layer_fun = NULL, |
| 17 |
+ jitter = FALSE, |
|
| 17 | 18 |
|
| 18 | 19 |
row_title = character(0), |
| 19 | 20 |
row_title_side = c("left", "right"),
|
| ... | ... |
@@ -106,6 +107,7 @@ Heatmap(matrix, col, name, |
| 106 | 107 |
\item{border}{Whether draw border. The value can be logical or a string of color.}
|
| 107 | 108 |
\item{cell_fun}{Self-defined function to add graphics on each cell. Seven parameters will be passed into this function: \code{j}, \code{i}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are column index, row index in \code{matrix}, coordinate of the cell, the width and height of the cell and the filled color. \code{x}, \code{y}, \code{width} and \code{height} are all \code{\link[grid]{unit}} objects.}
|
| 108 | 109 |
\item{layer_fun}{Similar as \code{cell_fun}, but is vectorized. Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#customize-the-heatmap-body} .}
|
| 110 |
+ \item{jitter}{Random shifts added to the matrix. The value can be logical or a single numeric value. It it is \code{TRUE}, random values from uniform distribution between 0 and 1e-10 are generated. If it is a numeric value, the range for the uniform distribution is (0, \code{jitter}). It is mainly to solve the problem of "Error: node stack overflow" when there are too many identical rows/columns for plotting the dendrograms.}
|
|
| 109 | 111 |
\item{row_title}{Title on the row.}
|
| 110 | 112 |
\item{row_title_side}{Will the title be put on the left or right of the heatmap?}
|
| 111 | 113 |
\item{row_title_gp}{Graphic parameters for row title.}
|
| ... | ... |
@@ -204,4 +206,5 @@ Zuguang Gu <z.gu@dkfz.de> |
| 204 | 206 |
\examples{
|
| 205 | 207 |
# There is no example |
| 206 | 208 |
NULL |
| 209 |
+ |
|
| 207 | 210 |
} |
| ... | ... |
@@ -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 |
} |
| ... | ... |
@@ -23,8 +24,8 @@ This function is only for internal use. |
| 23 | 24 |
\author{
|
| 24 | 25 |
Zuguang Gu <z.gu@dkfz.de> |
| 25 | 26 |
} |
| 26 |
-\alias{adjust_heatmap_list}
|
|
| 27 | 27 |
\examples{
|
| 28 | 28 |
# There is no example |
| 29 | 29 |
NULL |
| 30 |
+ |
|
| 30 | 31 |
} |
| ... | ... |
@@ -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 Legends |
| 5 | 6 |
} |
| ... | ... |
@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.
|
| 27 | 28 |
\author{
|
| 28 | 29 |
Zuguang Gu <z.gu@dkfz.de> |
| 29 | 30 |
} |
| 30 |
-\alias{annotation_legend_size}
|
|
| 31 | 31 |
\examples{
|
| 32 | 32 |
# There is no example |
| 33 | 33 |
NULL |
| 34 |
+ |
|
| 34 | 35 |
} |
| ... | ... |
@@ -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 Annotations |
| 5 | 6 |
} |
| ... | ... |
@@ -31,8 +32,8 @@ This function returns no value. |
| 31 | 32 |
\author{
|
| 32 | 33 |
Zuguang Gu <z.gu@dkfz.de> |
| 33 | 34 |
} |
| 34 |
-\alias{draw_annotation_legend}
|
|
| 35 | 35 |
\examples{
|
| 36 | 36 |
# There is no example |
| 37 | 37 |
NULL |
| 38 |
+ |
|
| 38 | 39 |
} |
| ... | ... |
@@ -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 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 |
} |
| ... | ... |
@@ -32,8 +33,8 @@ This function returns no value. |
| 32 | 33 |
\author{
|
| 33 | 34 |
Zuguang Gu <z.gu@dkfz.de> |
| 34 | 35 |
} |
| 35 |
-\alias{draw_heatmap_legend}
|
|
| 36 | 36 |
\examples{
|
| 37 | 37 |
# There is no example |
| 38 | 38 |
NULL |
| 39 |
+ |
|
| 39 | 40 |
} |
| ... | ... |
@@ -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 Legends |
| 5 | 6 |
} |
| ... | ... |
@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.
|
| 27 | 28 |
\author{
|
| 28 | 29 |
Zuguang Gu <z.gu@dkfz.de> |
| 29 | 30 |
} |
| 30 |
-\alias{heatmap_legend_size}
|
|
| 31 | 31 |
\examples{
|
| 32 | 32 |
# There is no example |
| 33 | 33 |
NULL |
| 34 |
+ |
|
| 34 | 35 |
} |
| ... | ... |
@@ -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 |
} |
| ... | ... |
@@ -28,8 +29,8 @@ A \code{\link{Heatmap-class}} object.
|
| 28 | 29 |
\author{
|
| 29 | 30 |
Zuguang Gu <z.gu@dkfz.de> |
| 30 | 31 |
} |
| 31 |
-\alias{make_column_cluster}
|
|
| 32 | 32 |
\examples{
|
| 33 | 33 |
# There is no example |
| 34 | 34 |
NULL |
| 35 |
+ |
|
| 35 | 36 |
} |
| ... | ... |
@@ -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{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{re_size-HeatmapAnnotation-method}
|
| 2 | 2 |
\alias{re_size,HeatmapAnnotation-method}
|
| 3 |
+\alias{re_size}
|
|
| 3 | 4 |
\title{
|
| 4 | 5 |
Resize the Width or Height of Heatmap Annotations |
| 5 | 6 |
} |
| ... | ... |
@@ -41,8 +42,8 @@ The basic rules are (take \code{height} and \code{annotation_height} for example
|
| 41 | 42 |
and \code{simple_anno_size} is disabled.
|
| 42 | 43 |
6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change.
|
| 43 | 44 |
} |
| 44 |
-\alias{re_size}
|
|
| 45 | 45 |
\examples{
|
| 46 | 46 |
# There is no example |
| 47 | 47 |
NULL |
| 48 |
+ |
|
| 48 | 49 |
} |
| ... | ... |
@@ -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 |
} |