Zuguang Gu authored on 18/01/2019 10:43:26 | ... | ... |
@@ -285,7 +285,11 @@ setMethod(f = "color_mapping_legend", |
| 285 | 285 |
e = environment() |
| 286 | 286 |
if(!is.null(param)) {
|
| 287 | 287 |
for(nm in names(param)) {
|
| 288 |
- assign(nm, param[[nm]], envir = e) |
|
| 288 |
+ if(nm == "direction") {
|
|
| 289 |
+ assign("legend_direction", param[[nm]], envir = e)
|
|
| 290 |
+ } else {
|
|
| 291 |
+ assign(nm, param[[nm]], envir = e) |
|
| 292 |
+ } |
|
| 289 | 293 |
} |
| 290 | 294 |
} |
| 291 | 295 |
|
| ... | ... |
@@ -394,6 +394,7 @@ Heatmap = function(matrix, col, name, |
| 394 | 394 |
show_row_dend = FALSE |
| 395 | 395 |
} |
| 396 | 396 |
row_dend_reorder = FALSE |
| 397 |
+ cluster_row_slices = FALSE |
|
| 397 | 398 |
|
| 398 | 399 |
if("clustering_distance_columns" %in% called_args) {
|
| 399 | 400 |
} else if(inherits(cluster_columns, c("dendrogram", "hclust"))) {
|
| ... | ... |
@@ -402,6 +403,7 @@ Heatmap = function(matrix, col, name, |
| 402 | 403 |
show_column_dend = FALSE |
| 403 | 404 |
} |
| 404 | 405 |
column_dend_reorder = FALSE |
| 406 |
+ cluster_column_slices = FALSE |
|
| 405 | 407 |
row_km = 1 |
| 406 | 408 |
column_km = 1 |
| 407 | 409 |
if(verbose) qqcat("matrix is character. Do not cluster unless distance method is provided.\n")
|
| ... | ... |
@@ -503,7 +503,7 @@ setMethod(f = "draw", |
| 503 | 503 |
} |
| 504 | 504 |
|
| 505 | 505 |
layout = grid.layout(nrow = length(HEATMAP_LIST_LAYOUT_COLUMN_COMPONENT), |
| 506 |
- ncol = length(HEATMAP_LAYOUT_ROW_COMPONENT), |
|
| 506 |
+ ncol = length(HEATMAP_LIST_LAYOUT_ROW_COMPONENT), |
|
| 507 | 507 |
widths = component_width(object), |
| 508 | 508 |
heights = component_height(object)) |
| 509 | 509 |
|
| ... | ... |
@@ -377,7 +377,6 @@ setMethod(f = "annotation_legend_size", |
| 377 | 377 |
}) |
| 378 | 378 |
|
| 379 | 379 |
# create a viewport which contains legend |
| 380 |
-# currently, one-row or one-column legend is supported |
|
| 381 | 380 |
draw_legend = function(ColorMappingList, ColorMappingParamList, side = c("right", "left", "top", "bottom"),
|
| 382 | 381 |
plot = TRUE, gap = unit(2, "mm"), legend_list = list(), padding = unit(c(0, 0, 0, 0), "mm"), |
| 383 | 382 |
max_height = unit(dev.size("cm")[2], "cm"), max_width = unit(dev.size("cm")[1], "cm"), ...) {
|
| ... | ... |
@@ -398,7 +397,7 @@ draw_legend = function(ColorMappingList, ColorMappingParamList, side = c("right"
|
| 398 | 397 |
if(side %in% c("left", "right")) {
|
| 399 | 398 |
pk = packLegend(list = cm_grob, gap = gap, direction = "vertical", max_height = max_height) |
| 400 | 399 |
} else {
|
| 401 |
- pk = packLegend(list = cm_grob, gap = gap, direction = "horizontal", max_width = max_width) |
|
| 400 |
+ pk = packLegend(list = cm_grob, gap = unit(4, "mm"), direction = "horizontal", max_width = max_width) |
|
| 402 | 401 |
} |
| 403 | 402 |
} |
| 404 | 403 |
|
| ... | ... |
@@ -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{anno_simple_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 |
} |