plot_coannotations {annotatr} | R Documentation |
All co-occurring annotations associated with a region are computed and displayed as a heatmap.
plot_coannotations( annotated_regions, annotation_order = NULL, plot_title, axes_label, quiet = FALSE )
annotated_regions |
The |
annotation_order |
A character vector which doubles as the subset of annotations desired for plot as well as the ordering. If |
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). |
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.
A ggplot
object which can be viewed by calling it, saved with ggplot2::ggsave
, or edited.
# 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')