plot_coannotations {annotatr} | R Documentation

## Plot pair-wise annotations across regions

### Description

All co-occurring annotations associated with a region are computed and displayed as a heatmap.

### Usage

    plot_coannotations(
      annotated_regions,
      annotation_order = NULL,
      plot_title,
      axes_label,
      quiet = FALSE
    )

### Arguments

`annotated_regions` | The `GRanges` result of `annotate_regions()`.
`annotation_order` | A character vector which doubles as the subset of annotations desired for plot as well as the ordering. If `NULL`, all annotations are displayed.
`plot_title` | A string used for the title of the plot. If missing, no plot title label is displayed.
`axes_label` | A string used for the axis labels. If missing, corresponding variable name used.
`quiet` | Print progress messages (FALSE) or not (TRUE).

### Details

As with `plot_annotation()`, the number in each cell is the number of unique regions annotated to the pair of annotations.

For example, if a region is annotated to both a CpG shore and to two different exons simultaneously, the region will only be counted once in the CpG shore / exon cell. NOTE, this same region will count once in both the CpG shore and exon cells on the diagonal.

### Value

A `ggplot` object which can be viewed by calling it, saved with `ggplot2::ggsave`, or edited.

### Examples

       # Get premade CpG annotations
       data('annotations', package = 'annotatr')

       dm_file = system.file('extdata', 'IDH2mut_v_NBM_multi_data_chr9.txt.gz', package = 'annotatr')
       extraCols = c(diff_meth = 'numeric', mu1 = 'numeric', mu0 = 'numeric')
       dm_regions = read_regions(con = dm_file, extraCols = extraCols,
           rename_score = 'pval', rename_name = 'DM_status', format = 'bed')
       dm_regions = dm_regions[1:1000]

       dm_annots = annotate_regions(
           regions = dm_regions,
           annotations = annotations,
           ignore.strand = TRUE)

       all_order = c(
           'hg19_cpg_islands',
           'hg19_cpg_shores',
           'hg19_cpg_shelves',
           'hg19_cpg_inter')

       dm_vs_ca = plot_coannotations(
           annotated_regions = dm_annots,
           annotation_order = all_order,
           axes_label = 'Annotations',
           plot_title = 'Co-occurrence of Annotations')

[Package annotatr version 1.16.0 Index]