plot_coannotations: Plot pair-wise annotations across regions

In rcavalcante/annotatr: Annotation of Genomic Regions to Genomic Annotations

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')

rcavalcante/annotatr documentation built on Aug. 22, 2024, 7:33 a.m.