Heatmap

Heatmap function from ComplexHeatmap. Credit to Dr. Zuguang Gu.

Heatmap(
  matrix,
  col,
  name = "value",
  na_col = "grey",
  color_space = "LAB",
  rect_gp = grid::gpar(col = NA),
  border = NA,
  border_gp = grid::gpar(col = "black"),
  cell_fun = NULL,
  layer_fun = NULL,
  jitter = FALSE,
  row_title = character(0),
  row_title_side = c("left", "right"),
  row_title_gp = grid::gpar(fontsize = 13.2),
  row_title_rot = switch(row_title_side[1], left = 90, right = 270),
  column_title = character(0),
  column_title_side = c("top", "bottom"),
  column_title_gp = grid::gpar(fontsize = 13.2),
  column_title_rot = 0,
  cluster_rows = TRUE,
  cluster_row_slices = TRUE,
  clustering_distance_rows = "euclidean",
  clustering_method_rows = "complete",
  row_dend_side = c("left", "right"),
  row_dend_width = unit(10, "mm"),
  show_row_dend = TRUE,
  row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows),
  row_dend_gp = grid::gpar(),
  cluster_columns = TRUE,
  cluster_column_slices = TRUE,
  clustering_distance_columns = "euclidean",
  clustering_method_columns = "complete",
  column_dend_side = c("top", "bottom"),
  column_dend_height = unit(10, "mm"),
  show_column_dend = TRUE,
  column_dend_gp = grid::gpar(),
  column_dend_reorder = is.logical(cluster_columns) || is.function(cluster_columns),
  row_order = NULL,
  column_order = NULL,
  row_labels = rownames(matrix),
  row_names_side = c("right", "left"),
  show_row_names = TRUE,
  row_names_max_width = unit(6, "cm"),
  row_names_gp = grid::gpar(fontsize = 12),
  row_names_rot = 0,
  row_names_centered = FALSE,
  column_labels = colnames(matrix),
  column_names_side = c("bottom", "top"),
  show_column_names = TRUE,
  column_names_max_height = unit(6, "cm"),
  column_names_gp = grid::gpar(fontsize = 12),
  column_names_rot = 90,
  column_names_centered = FALSE,
  top_annotation = NULL,
  bottom_annotation = NULL,
  left_annotation = NULL,
  right_annotation = NULL,
  km = 1,
  split = NULL,
  row_km = km,
  row_km_repeats = 1,
  row_split = split,
  column_km = 1,
  column_km_repeats = 1,
  column_split = NULL,
  gap = unit(1, "mm"),
  row_gap = unit(1, "mm"),
  column_gap = unit(1, "mm"),
  show_parent_dend_line = ComplexHeatmap::ht_opt$show_parent_dend_line,
  heatmap_width = unit(1, "npc"),
  width = NULL,
  heatmap_height = unit(1, "npc"),
  height = NULL,
  show_heatmap_legend = TRUE,
  heatmap_legend_param = list(title = name),
  use_raster = NULL,
  raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF",
    "agg_png"),
  raster_quality = 1,
  raster_device_param = list(),
  raster_resize_mat = FALSE,
  raster_by_magick = requireNamespace("magick", quietly = TRUE),
  raster_magick_filter = NULL,
  post_fun = NULL
)

Arguments

matrix

see ?ComplexHeatmap::Heatmap

col

see ?ComplexHeatmap::Heatmap

name

see ?ComplexHeatmap::Heatmap

na_col

see ?ComplexHeatmap::Heatmap

color_space

see ?ComplexHeatmap::Heatmap

rect_gp

see ?ComplexHeatmap::Heatmap

border

see ?ComplexHeatmap::Heatmap

border_gp

see ?ComplexHeatmap::Heatmap

cell_fun

see ?ComplexHeatmap::Heatmap

layer_fun

see ?ComplexHeatmap::Heatmap

jitter

see ?ComplexHeatmap::Heatmap

row_title

see ?ComplexHeatmap::Heatmap

row_title_side

see ?ComplexHeatmap::Heatmap

row_title_gp

see ?ComplexHeatmap::Heatmap

row_title_rot

see ?ComplexHeatmap::Heatmap

column_title

see ?ComplexHeatmap::Heatmap

column_title_side

see ?ComplexHeatmap::Heatmap

column_title_gp

see ?ComplexHeatmap::Heatmap

column_title_rot

see ?ComplexHeatmap::Heatmap

cluster_rows

see ?ComplexHeatmap::Heatmap

cluster_row_slices

see ?ComplexHeatmap::Heatmap

clustering_distance_rows

see ?ComplexHeatmap::Heatmap

clustering_method_rows

see ?ComplexHeatmap::Heatmap

row_dend_side

see ?ComplexHeatmap::Heatmap

row_dend_width

see ?ComplexHeatmap::Heatmap

show_row_dend

see ?ComplexHeatmap::Heatmap

row_dend_reorder

ee ?ComplexHeatmap::Heatmap

row_dend_gp

see ?ComplexHeatmap::Heatmap

cluster_columns

see ?ComplexHeatmap::Heatmap

cluster_column_slices

see ?ComplexHeatmap::Heatmap

clustering_distance_columns

see ?ComplexHeatmap::Heatmap

clustering_method_columns

see ?ComplexHeatmap::Heatmap

column_dend_side

see ?ComplexHeatmap::Heatmap

column_dend_height

see ?ComplexHeatmap::Heatmap

show_column_dend

see ?ComplexHeatmap::Heatmap

column_dend_gp

see ?ComplexHeatmap::Heatmap

column_dend_reorder

see ?ComplexHeatmap::Heatmap

row_order

see ?ComplexHeatmap::Heatmap

column_order

see ?ComplexHeatmap::Heatmap

row_labels

see ?ComplexHeatmap::Heatmap

row_names_side

see ?ComplexHeatmap::Heatmap

show_row_names

see ?ComplexHeatmap::Heatmap

row_names_max_width

see ?ComplexHeatmap::Heatmap

row_names_gp

see ?ComplexHeatmap::Heatmap

row_names_rot

see ?ComplexHeatmap::Heatmap

row_names_centered

see ?ComplexHeatmap::Heatmap

column_labels

see ?ComplexHeatmap::Heatmap

column_names_side

see ?ComplexHeatmap::Heatmap

show_column_names

see ?ComplexHeatmap::Heatmap

column_names_max_height

see ?ComplexHeatmap::Heatmap

column_names_gp

see ?ComplexHeatmap::Heatmap

column_names_rot

see ?ComplexHeatmap::Heatmap

column_names_centered

see ?ComplexHeatmap::Heatmap

top_annotation

see ?ComplexHeatmap::Heatmap

bottom_annotation

see ?ComplexHeatmap::Heatmap

left_annotation

see ?ComplexHeatmap::Heatmap

right_annotation

see ?ComplexHeatmap::Heatmap

km

see ?ComplexHeatmap::Heatmap

split

see ?ComplexHeatmap::Heatmap

row_km

see ?ComplexHeatmap::Heatmap

row_km_repeats

see ?ComplexHeatmap::Heatmap

row_split

see ?ComplexHeatmap::Heatmap

column_km

see ?ComplexHeatmap::Heatmap

column_km_repeats

see ?ComplexHeatmap::Heatmap

column_split

see ?ComplexHeatmap::Heatmap

gap

see ?ComplexHeatmap::Heatmap

row_gap

see ?ComplexHeatmap::Heatmap

column_gap

see ?ComplexHeatmap::Heatmap

show_parent_dend_line

see ?ComplexHeatmap::Heatmap

heatmap_width

see ?ComplexHeatmap::Heatmap

width

see ?ComplexHeatmap::Heatmap

heatmap_height

see ?ComplexHeatmap::Heatmap

height

see ?ComplexHeatmap::Heatmap

show_heatmap_legend

see ?ComplexHeatmap::Heatmap

heatmap_legend_param

see ?ComplexHeatmap::Heatmap

use_raster

see ?ComplexHeatmap::Heatmap

raster_device

see ?ComplexHeatmap::Heatmap

raster_quality

see ?ComplexHeatmap::Heatmap

raster_device_param

see ?ComplexHeatmap::Heatmap

raster_resize_mat

see ?ComplexHeatmap::Heatmap

raster_by_magick

see ?ComplexHeatmap::Heatmap

raster_magick_filter

see ?ComplexHeatmap::Heatmap

post_fun

see ?ComplexHeatmap::Heatmap

Value

A Heatmap-class object.

Author

Zuguang Gu z.gu@dkfz.de