Make Layout for the Heatmap List

Make Layout for the Heatmap List

# S4 method for 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(),

    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)

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.
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.

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.

Examples

# There is no example
NULL
#> NULL