HeatmapView: Draw heatmap

In WubingZhang/scAnalyzer: Integrative analysis pipeline for analyzing single-cell RNA-seq data

Draw heatmap

Description

Draw heatmap

Usage

HeatmapView(
  mat,
  breaks = c(-2, 0, 2),
  colors = c("blue", "#EEEEEE", "red"),
  na_col = "grey",
  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 = FALSE,
  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.
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.
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

No return.

Author(s)

Wubing Zhang

Examples

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)

WubingZhang/scAnalyzer documentation built on Jan. 30, 2023, 10:11 p.m.