Heatmap: Heatmap
In jaspershen/massstat: Statistical analysis for LC-MS-based metabolomics data

Heatmap

R Documentation

Heatmap

Description

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

Usage

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