Make Layout for the Heatmap List
Make Layout for the Heatmap List
## 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)
object |
A |
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 |
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 |
align_heatmap_legend |
How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". If the value is |
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 |
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 |
column_dend_side |
Similar setting as |
column_sub_title_side |
Similar setting as |
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 |
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. |
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.
A HeatmapList-class
object in which settings for all heatmap are adjusted.
Zuguang Gu <z.gu@dkfz.de>
# There is no example NULL
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