1. ComplexHeatmap
  2. man
  3. color_mapping_legend-ColorMapping-method.Rd
Browse code

add max_density argument

Zuguang Gu authored on 15/06/2022 10:42:56
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @c94e524
... ... 
@@ -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 
 }
... ... 
@@ -69,8 +70,8 @@ A \code{\link{Legends-class}} object.
69 70 
 \author{
70 71 
 Zuguang Gu <z.gu@dkfz.de>
71 72 
 }
72 
-\alias{color_mapping_legend}
73 73 
 \examples{
74 74 
 # There is no example
75 75 
 NULL
76 
+
76 77 
 }
Browse code

rename to anno_textbox()

Zuguang Gu authored on 15/06/2022 10:11:58
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @5cefa67
... ... 
@@ -1,6 +1,5 @@
1 1 
 \name{color_mapping_legend-ColorMapping-method}
2 2 
 \alias{color_mapping_legend,ColorMapping-method}
3 
-\alias{color_mapping_legend}
4 3 
 \title{
5 4 
 Draw Legend Based on Color Mapping
6 5 
 }
... ... 
@@ -70,8 +69,8 @@ A \code{\link{Legends-class}} object.
70 69 
 \author{
71 70 
 Zuguang Gu <z.gu@dkfz.de>
72 71 
 }
72 
+\alias{color_mapping_legend}
73 73 
 \examples{
74 74 
 # There is no example
75 75 
 NULL
76 
-
77 76 
 }
Browse code

add fontfamily/fontface to pheatmap()

Zuguang Gu authored on 10/05/2022 09:17:53
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @18765bd
... ... 
@@ -48,7 +48,7 @@ Draw Legend Based on Color Mapping
48 48 
   \item{border}{Color for legend grid borders. Pass to \code{\link{Legend}}.}
49 49 
   \item{at}{Break values of the legend. By default it is the levels in the \code{\link{ColorMapping-class}} object.}
50 50 
   \item{labels}{Labels corresponding to break values.}
51 
-  \item{labels_gp}{Graphical parameters for legend labels.}
51 
+  \item{labels_gp}{Graphcial parameters for legend labels.}
52 52 
   \item{labels_rot}{Rotation of labels.}
53 53 
   \item{nrow}{Pass to \code{\link{Legend}}. It controls the layout of legend grids if they are arranged in multiple rows or columns.}
54 54 
   \item{ncol}{Pass to \code{\link{Legend}}. It controls the layout of legend grids if they are arranged in multiple rows or columns.}
Browse code

Update color_mapping_legend-ColorMapping-method.Rd

Goultard59 authored on 08/04/2022 13:05:41 • GitHub committed on 08/04/2022 13:05:41
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @641da76
... ... 
@@ -48,7 +48,7 @@ Draw Legend Based on Color Mapping
48 48 
   \item{border}{Color for legend grid borders. Pass to \code{\link{Legend}}.}
49 49 
   \item{at}{Break values of the legend. By default it is the levels in the \code{\link{ColorMapping-class}} object.}
50 50 
   \item{labels}{Labels corresponding to break values.}
51 
-  \item{labels_gp}{Graphcial parameters for legend labels.}
51 
+  \item{labels_gp}{Graphical parameters for legend labels.}
52 52 
   \item{labels_rot}{Rotation of labels.}
53 53 
   \item{nrow}{Pass to \code{\link{Legend}}. It controls the layout of legend grids if they are arranged in multiple rows or columns.}
54 54 
   \item{ncol}{Pass to \code{\link{Legend}}. It controls the layout of legend grids if they are arranged in multiple rows or columns.}
Browse code

won't generate color matrix when type=='none'

Zuguang Gu authored on 15/12/2020 12:01:39
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @110a6d6
... ... 
@@ -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 
 }
... ... 
@@ -69,8 +70,8 @@ A \code{\link{Legends-class}} object.
69 70 
 \author{
70 71 
 Zuguang Gu <z.gu@dkfz.de>
71 72 
 }
72 
-\alias{color_mapping_legend}
73 73 
 \examples{
74 74 
 # There is no example
75 75 
 NULL
76 
+
76 77 
 }
Browse code

translate stats::heatmap() and gplots::heatmap.2()

Zuguang Gu authored on 13/12/2020 20:54:51
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @2f64420
... ... 
@@ -1,6 +1,5 @@
1 1 
 \name{color_mapping_legend-ColorMapping-method}
2 2 
 \alias{color_mapping_legend,ColorMapping-method}
3 
-\alias{color_mapping_legend}
4 3 
 \title{
5 4 
 Draw Legend Based on Color Mapping
6 5 
 }
... ... 
@@ -70,8 +69,8 @@ A \code{\link{Legends-class}} object.
70 69 
 \author{
71 70 
 Zuguang Gu <z.gu@dkfz.de>
72 71 
 }
72 
+\alias{color_mapping_legend}
73 73 
 \examples{
74 74 
 # There is no example
75 75 
 NULL
76 
-
77 76 
 }
Browse code

update

Zuguang Gu authored on 03/11/2020 13:57:14
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @efb83b6
... ... 
@@ -29,7 +29,7 @@ Draw Legend Based on Color Mapping
29 29 
     legend_height = NULL,
30 30 
     legend_width = NULL,
31 31 
     legend_direction = c("vertical", "horizontal"),
32 
-    interval_dist = NULL,
32 
+    break_dist = NULL,
33 33
34 34 
     graphics = NULL,
35 35 
     param = NULL)
... ... 
@@ -56,7 +56,7 @@ Draw Legend Based on Color Mapping
56 56 
   \item{legend_height}{Height of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{vertical}. Pass to \code{\link{Legend}}.}
57 57 
   \item{legend_width}{Width of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{horizontal}. Pass to \code{\link{Legend}}.}
58 58 
   \item{legend_direction}{When \code{color_bar} is \code{continuous}, whether the legend is vertical or horizontal? Pass to \code{\link{Legend}}.}
59 
-  \item{interval_dist}{A zooming factor to control relative distance of two neighbouring break values.The length of it should be \code{length(at) - 1} or a scalar. }
59 
+  \item{break_dist}{A zooming factor to control relative distance of two neighbouring break values.The length of it should be \code{length(at) - 1} or a scalar. }
60 60 
   \item{graphics}{Internally used.}
61 61 
   \item{param}{All the legend-related parameters can be specified as a single list.}
62 62
Browse code

adjust positions of breaks in the legend

Zuguang Gu authored on 02/11/2020 20:21:10
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @59dafee
... ... 
@@ -29,6 +29,7 @@ Draw Legend Based on Color Mapping
29 29 
     legend_height = NULL,
30 30 
     legend_width = NULL,
31 31 
     legend_direction = c("vertical", "horizontal"),
32 
+    interval_dist = NULL,
32 33
33 34 
     graphics = NULL,
34 35 
     param = NULL)
... ... 
@@ -55,6 +56,7 @@ Draw Legend Based on Color Mapping
55 56 
   \item{legend_height}{Height of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{vertical}. Pass to \code{\link{Legend}}.}
56 57 
   \item{legend_width}{Width of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{horizontal}. Pass to \code{\link{Legend}}.}
57 58 
   \item{legend_direction}{When \code{color_bar} is \code{continuous}, whether the legend is vertical or horizontal? Pass to \code{\link{Legend}}.}
59 
+  \item{interval_dist}{A zooming factor to control relative distance of two neighbouring break values.The length of it should be \code{length(at) - 1} or a scalar. }
58 60 
   \item{graphics}{Internally used.}
59 61 
   \item{param}{All the legend-related parameters can be specified as a single list.}
60 62
Browse code

various improvements

Zuguang Gu authored on 23/10/2020 16:02:23
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @8b0c851
... ... 
@@ -30,6 +30,7 @@ Draw Legend Based on Color Mapping
30 30 
     legend_width = NULL,
31 31 
     legend_direction = c("vertical", "horizontal"),
32 32
33 
+    graphics = NULL,
33 34 
     param = NULL)
34 35 
 }
35 36 
 \arguments{
... ... 
@@ -54,6 +55,7 @@ Draw Legend Based on Color Mapping
54 55 
   \item{legend_height}{Height of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{vertical}. Pass to \code{\link{Legend}}.}
55 56 
   \item{legend_width}{Width of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{horizontal}. Pass to \code{\link{Legend}}.}
56 57 
   \item{legend_direction}{When \code{color_bar} is \code{continuous}, whether the legend is vertical or horizontal? Pass to \code{\link{Legend}}.}
58 
+  \item{graphics}{Internally used.}
57 59 
   \item{param}{All the legend-related parameters can be specified as a single list.}
58 60
59 61 
 }
Browse code

update

Zuguang Gu authored on 20/10/2019 06:57:30
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @7abc442
... ... 
@@ -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 
 }
Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
Showing1 changed files
man/color_mapping_legend-ColorMapping-method.Rd
History View file @1cb7fea
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,72 @@
1 
+\name{color_mapping_legend-ColorMapping-method}
2 
+\alias{color_mapping_legend,ColorMapping-method}
3 
+\title{
4 
+Draw Legend Based on Color Mapping
5 
+}
6 
+\description{
7 
+Draw Legend Based on Color Mapping
8 
+}
9 
+\usage{
10 
+\S4method{color_mapping_legend}{ColorMapping}(object,
11 
+    plot = TRUE, ...,
12 
+
13 
+    color_bar = object@type,
14 
+
15 
+    title = object@name,
16 
+    title_gp = gpar(fontsize = 10, fontface = "bold"),
17 
+    title_position = "topleft",
18 
+    grid_height = unit(4, "mm"),
19 
+    grid_width = unit(4, "mm"),
20 
+    border = NULL,
21 
+    at = object@levels,
22 
+    labels = at,
23 
+    labels_gp = gpar(fontsize = 10),
24 
+    labels_rot = 0,
25 
+    nrow = NULL,
26 
+    ncol = 1,
27 
+    by_row = FALSE,
28 
+    legend_height = NULL,
29 
+    legend_width = NULL,
30 
+    legend_direction = c("vertical", "horizontal"),
31 
+
32 
+    param = NULL)
33 
+}
34 
+\arguments{
35 
+
36 
+  \item{object}{A \code{\link{ColorMapping-class}} object.}
37 
+  \item{plot}{Whether to plot or just return the legend object?}
38 
+  \item{...}{Pass to \code{\link{draw,Legends-method}}.}
39 
+  \item{color_bar}{"continous" or "discrete". It controls whether to show the discrete legend for the continuous color mapping.}
40 
+  \item{title}{Title of the legend, by default it is the name of the legend.}
41 
+  \item{title_gp}{Graphical parameters for legend title.}
42 
+  \item{title_position}{Position of the title. See \code{\link{Legend}} for all possible values.}
43 
+  \item{grid_height}{Height of each legend grid. Pass to \code{\link{Legend}}.}
44 
+  \item{grid_width}{Width of each legend grid. Pass to \code{\link{Legend}}.}
45 
+  \item{border}{Color for legend grid borders. Pass to \code{\link{Legend}}.}
46 
+  \item{at}{Break values of the legend. By default it is the levels in the \code{\link{ColorMapping-class}} object.}
47 
+  \item{labels}{Labels corresponding to break values.}
48 
+  \item{labels_gp}{Graphcial parameters for legend labels.}
49 
+  \item{labels_rot}{Rotation of labels.}
50 
+  \item{nrow}{Pass to \code{\link{Legend}}. It controls the layout of legend grids if they are arranged in multiple rows or columns.}
51 
+  \item{ncol}{Pass to \code{\link{Legend}}. It controls the layout of legend grids if they are arranged in multiple rows or columns.}
52 
+  \item{by_row}{Pass to \code{\link{Legend}}. It controls the order of legend grids if they are arranged in multiple rows or columns.}
53 
+  \item{legend_height}{Height of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{vertical}. Pass to \code{\link{Legend}}.}
54 
+  \item{legend_width}{Width of the legend body. It only works when \code{color_bar} is \code{continuous} and \code{direction} is \code{horizontal}. Pass to \code{\link{Legend}}.}
55 
+  \item{legend_direction}{When \code{color_bar} is \code{continuous}, whether the legend is vertical or horizontal? Pass to \code{\link{Legend}}.}
56 
+  \item{param}{All the legend-related parameters can be specified as a single list.}
57 
+
58 
+}
59 
+\details{
60 
+The legend is constructed by \code{\link{Legend}}.
61 
+}
62 
+\value{
63 
+A \code{\link{Legends-class}} object.
64 
+}
65 
+\author{
66 
+Zuguang Gu <z.gu@dkfz.de>
67 
+}
68 
+\alias{color_mapping_legend}
69 
+\examples{
70 
+# There is no example
71 
+NULL
72 
+}