Draw a list of heatmaps

Draw a list of heatmaps

# S4 method for HeatmapList
draw(object,
    newpage = TRUE,

    row_title = character(0),
    row_title_side = c("left", "right"),
    row_title_gp = gpar(fontsize = 14),
    column_title = character(0),
    column_title_side = c("top", "bottom"),
    column_title_gp = gpar(fontsize = 14),

    heatmap_legend_side = c("right", "left", "bottom", "top"),
    merge_legends = FALSE,
    show_heatmap_legend = TRUE,
    heatmap_legend_list = list(),
    annotation_legend_side = c("right", "left", "bottom", "top"),
    show_annotation_legend = TRUE,
    annotation_legend_list = list(),

    gap = unit(2, "mm"),
    ht_gap = gap,

    main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],
    padding = GLOBAL_PADDING,
    adjust_annotation_extension = NULL,

    auto_adjust = TRUE,
    row_dend_side = c("original", "left", "right"),
    row_sub_title_side = c("original", "left", "right"),
    column_dend_side = c("original", "top", "bottom"),
    column_sub_title_side = c("original", "top", "bottom"),

    row_gap = NULL,
    cluster_rows = NULL,
    cluster_row_slices = NULL,
    clustering_distance_rows = NULL,
    clustering_method_rows = NULL,
    row_dend_width = NULL,
    show_row_dend = NULL,
    row_dend_reorder = NULL,
    row_dend_gp = NULL,
    row_order = NULL,
    km = NULL,
    split = NULL,
    row_km = km,
    row_km_repeats = NULL,
    row_split = split,
    height = NULL,
    heatmap_height = NULL,

    column_gap = NULL,
    cluster_columns = NULL,
    cluster_column_slices = NULL,
    clustering_distance_columns = NULL,
    clustering_method_columns = NULL,
    column_dend_width = NULL,
    show_column_dend = NULL,
    column_dend_reorder = NULL,
    column_dend_gp = NULL,
    column_order = NULL,
    column_km = NULL,
    column_km_repeats = NULL,
    column_split = NULL,
    width = NULL,
    heatmap_width = NULL,

    ### global setting
    heatmap_row_names_gp = NULL,
    heatmap_column_names_gp = NULL,
    heatmap_row_title_gp = NULL,
    heatmap_column_title_gp = NULL,
    legend_title_gp = NULL,
    legend_title_position = NULL,
    legend_labels_gp = NULL,
    legend_grid_height = NULL,
    legend_grid_width = NULL,
    legend_border = NULL,
    heatmap_border = NULL,
    annotation_border = NULL,
    fastcluster = NULL,
    simple_anno_size = NULL,
    show_parent_dend_line = NULL)

Arguments

object	a HeatmapList-class object.
newpage	whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use grid.grabExpr.
row_title	title on the row.
row_title_side	will the title be put on the left or right of the heatmap.
row_title_gp	graphic parameters for drawing text.
column_title	title on the column.
column_title_side	will the title be put on the top or bottom of the heatmap.
column_title_gp	graphic parameters for drawing text.
heatmap_legend_side	side to put heatmap legend
merge_legends	merge heatmap legends and annotation legends to put into one column.
show_heatmap_legend	whether show all heatmap legends
heatmap_legend_list	use-defined legends which are put after the heatmap legends
annotation_legend_side	side of the annotation legends
show_annotation_legend	whether show annotation legends
annotation_legend_list	user-defined legends which are put after the annotation legends
gap	gap between heatmaps/annotations
ht_gap	same as gap.
main_heatmap	index of main heatmap. The value can be a numeric index or the heatmap name
padding	padding of the whole plot. The value is a unit vector of length 4, which corresponds to bottom, left, top and right.
adjust_annotation_extension	whether take annotation name into account when calculating positions of graphic elements.
auto_adjust	whether apply automatic adjustment? The auto-adjustment includes turning off dendrograms, titles and row/columns for non-main heatmaps.
row_dend_side	side of the dendrogram from the main heatmap
row_sub_title_side	side of the row title from the main heatmap
column_dend_side	side of the dendrogram from the main heatmap
column_sub_title_side	side of the column title from the main heatmap
row_gap	this modifies row_gap of the main heatmap
cluster_rows	this modifies cluster_rows of the main heatmap
cluster_row_slices	this modifies cluster_row_slices of the main heatmap
clustering_distance_rows	this modifies clustering_distance_rows of the main heatmap
clustering_method_rows	this modifies clustering_method_rows of the main heatmap
row_dend_width	this modifies row_dend_width of the main heatmap
show_row_dend	this modifies show_row_dend of the main heatmap
row_dend_reorder	this modifies row_dend_reorder of the main heatmap
row_dend_gp	this modifies row_dend_gp of the main heatmap
row_order	this modifies row_order of the main heatmap
km	= this modifies km of the main heatmap
split	this modifies split of the main heatmap
row_km	this modifies row_km of the main heatmap
row_km_repeats	this modifies row_km_repeats of the main heatmap
row_split	this modifies row_split of the main heatmap
height	this modifies height of the main heatmap
heatmap_height	this modifies heatmap_height of the main heatmap
column_gap	this modifies column_gap of the main heatmap
cluster_columns	this modifies cluster_columns of the main heatmap
cluster_column_slices	this modifies cluster_column_slices of the main heatmap
clustering_distance_columns	this modifies clustering_distance_columns of the main heatmap
clustering_method_columns	this modifies clustering_method_columns of the main heatmap
column_dend_width	this modifies column_dend_width of the main heatmap
show_column_dend	this modifies show_column_dend of the main heatmap
column_dend_reorder	this modifies column_dend_reorder of the main heatmap
column_dend_gp	this modifies column_dend_gp of the main heatmap
column_order	this modifies column_order of the main heatmap
column_km	this modifies column_km of the main heatmap
column_km_repeats	this modifies column_km_repeats of the main heatmap
column_split	this modifies column_split of the main heatmap
width	this modifies width of the main heatmap
heatmap_width	this modifies heatmap_width of the main heatmap
heatmap_row_names_gp	this set the value in ht_opt and reset back after the plot is done
heatmap_column_names_gp	this set the value in ht_opt and reset back after the plot is done
heatmap_row_title_gp	this set the value in ht_opt and reset back after the plot is done
heatmap_column_title_gp	this set the value in ht_opt and reset back after the plot is done
legend_title_gp	this set the value in ht_opt and reset back after the plot is done
legend_title_position	this set the value in ht_opt and reset back after the plot is done
legend_labels_gp	this set the value in ht_opt and reset back after the plot is done
legend_grid_height	this set the value in ht_opt and reset back after the plot is done
legend_grid_width	this set the value in ht_opt and reset back after the plot is done
legend_border	this set the value in ht_opt and reset back after the plot is done
heatmap_border	this set the value in ht_opt and reset back after the plot is done
annotation_border	this set the value in ht_opt and reset back after the plot is done
fastcluster	this set the value in ht_opt and reset back after the plot is done
simple_anno_size	this set the value in ht_opt and reset back after the plot is done
show_parent_dend_line	this set the value in ht_opt and reset back after the plot is done

Details

The function first calls make_layout,HeatmapList-method to calculate the layout of the heatmap list and the layout of every single heatmap, then makes the plot by re-calling the graphic functions which are already recorded in the layout.

See also

https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html

Value

This function returns a HeatmapList-class object for which the layout has been created.

Examples

# There is no example
NULL
#> NULL