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pheatmap.Rd
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\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
}