1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
|
\name{pheatmap}
\alias{pheatmap}
\title{
Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap
}
\description{
Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap
}
\usage{
pheatmap(mat,
color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100),
kmeans_k = NA,
breaks = NA,
border_color = ifelse(nrow(mat) < 100 & ncol(mat) < 100, "grey60", NA),
cellwidth = NA,
cellheight = NA,
scale = "none",
cluster_rows = TRUE,
cluster_cols = TRUE,
clustering_distance_rows = "euclidean",
clustering_distance_cols = "euclidean",
clustering_method = "complete",
clustering_callback = NA,
cutree_rows = NA,
cutree_cols = NA,
treeheight_row = ifelse(class(cluster_rows) == "hclust" || cluster_rows, 50, 0),
treeheight_col = ifelse(class(cluster_cols) == "hclust" || cluster_cols, 50, 0),
legend = TRUE,
legend_breaks = NA,
legend_labels = NA,
annotation_row = NA,
annotation_col = NA,
annotation = NA,
annotation_colors = NA,
annotation_legend = TRUE,
annotation_names_row = TRUE,
annotation_names_col = TRUE,
drop_levels = TRUE,
show_rownames = TRUE,
show_colnames = TRUE,
main = NA,
fontsize = 10,
fontsize_row = fontsize,
fontsize_col = fontsize,
angle_col = c("270", "0", "45", "90", "315"),
display_numbers = FALSE,
number_format = "\%.2f",
number_color = "grey30",
fontsize_number = 0.8 * fontsize,
gaps_row = NULL,
gaps_col = NULL,
labels_row = NULL,
labels_col = NULL,
filename = NA,
width = NA,
height = NA,
silent = FALSE,
na_col = "#DDDDDD",
name = NULL,
# other graphic parameters for fonts
fontfamily = "",
fontfamily_row = fontfamily,
fontfamily_col = fontfamily,
fontface = 1,
fontface_row = fontface,
fontface_col = fontface,
# argument specific for Heatmap()
heatmap_legend_param = list(),
...,
run_draw = FALSE)
}
\arguments{
\item{mat}{The input matrix.}
\item{color}{The same as in \code{\link[pheatmap]{pheatmap}}. Here you don't necessarily need to generate a long color vector. The discrete colors sent to \code{\link[grDevices:colorRamp]{colorRampPalette}} are also OK here. E.g. \code{colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100)} can be simply replaced as \code{rev(brewer.pal(n = 7, name = "RdYlBu"))}.}
\item{kmeans_k}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{breaks}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{border_color}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{cellwidth}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{cellheight}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{scale}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{cluster_rows}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{cluster_cols}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{clustering_distance_rows}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{clustering_distance_cols}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{clustering_method}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{clustering_callback}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{cutree_rows}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{cutree_cols}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{treeheight_row}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{treeheight_col}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{legend}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{legend_breaks}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{legend_labels}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{annotation_row}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{annotation_col}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{annotation}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{annotation_colors}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{annotation_legend}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{annotation_names_row}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{annotation_names_col}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{drop_levels}{Enforced to be \code{TRUE}.}
\item{show_rownames}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{show_colnames}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{main}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{fontsize}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{fontsize_row}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{fontsize_col}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{angle_col}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{display_numbers}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{number_format}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{number_color}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{fontsize_number}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{gaps_row}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{gaps_col}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{labels_row}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{labels_col}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{filename}{Not supported.}
\item{width}{Not supported.}
\item{height}{Not supported.}
\item{silent}{Not supported.}
\item{na_col}{The same as in \code{\link[pheatmap]{pheatmap}}.}
\item{name}{Name of the heatmap. This argument is passed to \code{\link{Heatmap}}.}
\item{fontfamily}{Font family for row and column names.}
\item{fontfamily_row}{Font family for row names.}
\item{fontfamily_col}{Font family for column names.}
\item{fontface}{Font face for row and column names.}
\item{fontface_row}{Font face for row names.}
\item{fontface_col}{Font face for column names.}
\item{heatmap_legend_param}{Pass to \code{\link{Heatmap}}.}
\item{...}{Other arguments passed to \code{\link{Heatmap}}.}
\item{run_draw}{Whether to run \code{draw()} function to the heatmap object.}
}
\details{
This function aims to execute \code{pheatmap::pheatmap} code purely with ComplexHeatmap.
}
\seealso{
See \url{https://jokergoo.github.io/2020/05/06/translate-from-pheatmap-to-complexheatmap/}
\code{\link{compare_pheatmap}} that compares heatmaps between \code{pheatmap::pheatmap()} and \code{ComplexHeatmap::pheatmap()}.
}
\value{
A \code{\link{Heatmap-class}} object.
}
\examples{
# There is no example
NULL
}
|
