make_layout-HeatmapList-method {ComplexHeatmap} | R Documentation

## Make Layout for the Heatmap List

### Description

Make Layout for the Heatmap List

### Usage

    ## S4 method for signature 'HeatmapList'
    make_layout(object,

        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(),
        align_heatmap_legend = NULL,
        align_annotation_legend = NULL,
        legend_grouping = c("adjusted", "original"),

        ht_gap = unit(2, "mm"),

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

        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,
        row_km = NULL,
        row_km_repeats = NULL,
        row_split = NULL,
        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,

        use_raster = NULL,
        raster_device = NULL,
        raster_quality = NULL,
        raster_device_param = NULL,
        raster_resize = NULL)

### Arguments

`object` | A `HeatmapList-class` object.
`row_title` | Title on the row.
`row_title_side` | Will the title be put on the left or right of the heatmap list?
`row_title_gp` | Graphic parameters for the row title.
`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 the column title.
`heatmap_legend_side` | Side of the heatmap legends.
`merge_legends` | Whether to put heatmap legends and annotation legends together. By default they are put in different viewports.
`show_heatmap_legend` | Whether show heatmap legends.
`heatmap_legend_list` | A list of self-defined legends, should be wrapped into a list of `grob` objects. Normally they are constructed by `Legend`.
`annotation_legend_side` | Side of annotation legends.
`show_annotation_legend` | Whether show annotation legends.
`annotation_legend_list` | A list of self-defined legends, should be wrapped into a list of `grob` objects. Normally they are constructed by `Legend`.
`align_heatmap_legend` | How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". If the value is `NULL`, it automatically picks the proper value from the three options.
`align_annotation_legend` | How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center".
`legend_grouping` | How the legends are grouped. Values should be "adjusted" or "original".
`ht_gap` | Gap between heatmaps, should be a `unit` object. It can be a vector of length 1 or the number of heamtaps/annotations.
`main_heatmap` | Name or index for the main heatmap.
`padding` | Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings.
`auto_adjust` | whether apply automatic adjustment? The auto-adjustment includes turning off dendrograms, titles and row/columns for non-main heatmaps.
`row_dend_side` | If auto-adjustment is on, to put the row dendrograms of the main heatmap to the most left side of the heatmap list or the most right side?
`row_sub_title_side` | There can be sub titles generated by the splitting of heatmaps. Similar setting as `row_dend_side`.
`column_dend_side` | Similar setting as `row_dend_side`.
`column_sub_title_side` | Similar setting as `row_sub_title_side`.
`row_gap` | Overwrite the corresponding setting in the main heatmap.
`cluster_rows` | Overwrite the corresponding setting in the main heatmap.
`cluster_row_slices` | Overwrite the corresponding setting in the main heatmap.
`clustering_distance_rows` | Overwrite the corresponding setting in the main heatmap.
`clustering_method_rows` | Overwrite the corresponding setting in the main heatmap.same setting as in `Heatmap`, if it is specified, `clustering_method_rows` in main heatmap is ignored.
`row_dend_width` | Overwrite the corresponding setting in the main heatmap.
`show_row_dend` | same Overwrite the corresponding setting in the main heatmap.
`row_dend_reorder` | Overwrite the corresponding setting in the main heatmap.
`row_dend_gp` | Overwrite the corresponding setting in the main heatmap.
`row_order` | Overwrite the corresponding setting in the main heatmap.
`row_km` | Overwrite the corresponding setting in the main heatmap.
`row_km_repeats` | Overwrite the corresponding setting in the main heatmap.
`row_split` | Overwrite the corresponding setting in the main heatmap.
`height` | Overwrite the corresponding setting in the main heatmap.
`heatmap_height` | Overwrite the corresponding setting in the main heatmap.
`column_gap` | Overwrite the corresponding setting in the main heatmap.
`cluster_columns` | Overwrite the corresponding setting in the main heatmap.
`cluster_column_slices` | Overwrite the corresponding setting in the main heatmap.
`clustering_distance_columns` | Overwrite the corresponding setting in the main heatmap.
`clustering_method_columns` | Overwrite the corresponding setting in the main heatmap.
`column_dend_width` | column Overwrite the corresponding setting in the main heatmap.
`show_column_dend` | Overwrite the corresponding setting in the main heatmap.
`column_dend_reorder` | Overwrite the corresponding setting in the main heatmap.
`column_dend_gp` | Overwrite the corresponding setting in the main heatmap.
`column_order` | Overwrite the corresponding setting in the main heatmap.
`column_km` | Overwrite the corresponding setting in the main heatmap.
`column_km_repeats` | Overwrite the corresponding setting in the main heatmap.
`column_split` | Overwrite the corresponding setting in the main heatmap.
`width` | Overwrite the corresponding setting in the main heatmap.
`heatmap_width` | Overwrite the corresponding setting in the main heatmap.
`use_raster` | Overwrite the corresponding setting in every heatmap.
`raster_device` | Overwrite the corresponding setting in every heatmap.
`raster_quality` | Overwrite the corresponding setting in every heatmap.
`raster_device_param` | Overwrite the corresponding setting in every heatmap.
`raster_resize` | Overwrite the corresponding setting in every heatmap.

### Details

It sets the size of each component of the heatmap list and adjusts graphic parameters for each heatmap if necessary.

This function is only for internal use.

### Value

A `HeatmapList-class` object in which settings for all heatmap are adjusted.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    # There is no example
    NULL

[Package ComplexHeatmap version 2.10.0 Index]