Skip to contents

Draw Heatmap

Source: R/HeatmapView.R
HeatmapView.Rd

Draw Heatmap

Usage

HeatmapView(
  mat,
  breaks = c(0, 0.6, 1.2),
  colors = c("#ffffd9", "#edf8b1", "#225ea8"),
  na_col = "grey",
  name = "hmap",
  cluster_rows = FALSE,
  row_dend_side = c("left", "right"),
  cluster_cols = FALSE,
  column_dend_side = c("top", "bottom"),
  show_row_names = TRUE,
  row_names_side = "left",
  row_names_gp = gpar(fontsize = 12),
  row_names_rot = 0,
  show_column_names = TRUE,
  column_names_side = "bottom",
  column_names_gp = gpar(fontsize = 12),
  column_names_rot = 90,
  show_legend = TRUE,
  top_ann = NULL,
  top_ann_col = NULL,
  show_top_legend = show_legend,
  bott_ann = NULL,
  bott_ann_col = NULL,
  show_bott_legend = show_legend,
  left_ann = NULL,
  left_ann_col = NULL,
  show_left_legend = show_legend,
  right_ann = NULL,
  right_ann_col = NULL,
  show_right_legend = show_legend,
  show_ann_name = TRUE,
  annotation_legend_param = list(),
  row_split = NULL,
  column_split = NULL,
  show_heatmap_legend = TRUE,
  legend_title = NULL,
  legend_title_position = "lefttop",
  legend_direction = "vertical",
  legend_title_gp = gpar(fontsize = 12),
  legend_labels_gp = gpar(fontsize = 12),
  legend_height = 2,
  legend_width = 0.3,
  legend_side = "right",
  ...
)

Arguments

mat

Matrix like object.

breaks

A vector indicating numeric breaks.

colors

A vector of colors which correspond to values in breaks.

na_col

Color for NA values.

name

Heatmap name.

cluster_rows

Same as that in ComplexHeatmap::Heatmap.

row_dend_side

Same as that in ComplexHeatmap::Heatmap.

cluster_cols

Same as that in ComplexHeatmap::Heatmap.

column_dend_side

Same as that in ComplexHeatmap::Heatmap.

show_row_names

Same as that in ComplexHeatmap::Heatmap.

row_names_side

Same as that in ComplexHeatmap::Heatmap.

row_names_gp

Same as that in ComplexHeatmap::Heatmap.

row_names_rot

Same as that in ComplexHeatmap::Heatmap.

show_column_names

Same as that in ComplexHeatmap::Heatmap.

column_names_side

Same as that in ComplexHeatmap::Heatmap.

column_names_gp

Same as that in ComplexHeatmap::Heatmap.

column_names_rot

Same as that in ComplexHeatmap::Heatmap.

show_legend

Whether show annotation legends.

top_ann

A data frame. Each column will be treated as a simple annotation. The data frame must have column names. Can also be a HeatmapAnnotation-class object.

top_ann_col

A list of colors which contain color mapping to df.

show_top_legend

Whether show annotation legends.

bott_ann

Same as top_ann.

bott_ann_col

A list of colors which contain color mapping to df.

show_bott_legend

Whether show annotation legends.

left_ann

Same as top_ann.

left_ann_col

A list of colors which contain color mapping to df.

show_left_legend

Whether show annotation legends.

right_ann

Same as top_ann.

right_ann_col

A list of colors which contain color mapping to df.

show_right_legend

Whether show annotation legends.

show_ann_name

Whether show annotation names.

annotation_legend_param

A list which contains parameters for annotation legends.

row_split

A vector or a data frame by which the rows are split. But if cluster_rows is a clustering object, split can be a single number indicating to split the dendrogram by cutree.

column_split

Same as row_split.

show_heatmap_legend

Whether show legends.

legend_title

Character specifyin the legend title.

legend_title_position

Position of title relative to the legend. topleft, topcenter, leftcenter-rot and lefttop-rot are only for vertical legend and leftcenter, lefttop are only for horizontal legend.

legend_direction

Vertical or horizontal?

legend_title_gp

Graphic parameters of the title.

legend_labels_gp

Graphic parameters for labels.

legend_height

Height of the whole legend body. It is only used for vertical continous legend.

legend_width

Width of the whole legend body. It is only used for horizontal continous legend.

legend_side

Side to put heatmap legend

...

Other parameters in draw.

Value

A `Heatmap-class` object.

Author

Wubing Zhang

Examples

library(grid)
library(SpatialEcoTyper)
library(ComplexHeatmap)
#> ========================================
#> ComplexHeatmap version 2.20.0
#> Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
#> Github page: https://github.com/jokergoo/ComplexHeatmap
#> Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
#> 
#> If you use it in published research, please cite either one:
#> - Gu, Z. Complex Heatmap Visualization. iMeta 2022.
#> - Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
#>     genomic data. Bioinformatics 2016.
#> 
#> 
#> The new InteractiveComplexHeatmap package can directly export static 
#> complex heatmaps into an interactive Shiny app with zero effort. Have a try!
#> 
#> This message can be suppressed by:
#>   suppressPackageStartupMessages(library(ComplexHeatmap))
#> ========================================

dat = matrix(rnorm(100), 10)
rownames(dat) = letters[1:10]
colnames(dat) = letters[11:20]
rowann = data.frame(Group = rep(letters[1:2], each=5), index = 1:10)
colann = data.frame(Group = rep(letters[1:2], each=5), index = 11:20)
HeatmapView(dat, left_ann = rowann, top_ann = colann)
#> Loading required package: pals