draw-HeatmapList-method: Draw a list of heatmaps
In zhongmicai/complexHeatmap: Make Complex Heatmaps

Description Usage Arguments Details Value Author(s) See Also Examples

Draw a list of heatmaps

## S4 method for signature '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,
    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,
    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)

`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
`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
`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

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.

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

Zuguang Gu <z.gu@dkfz.de>

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