plot_numerical_coannotations: Plot numerical data occurring in pairs of annotations

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

Plot numerical data occurring in pairs of annotations

Description

Plot numerical data associated with regions occurring in annot1, annot2 and in both. As with plot_numerical(), the result is a plot of histograms or x-y scatterplots.

Usage

plot_numerical_coannotations(
  annotated_regions,
  x,
  y,
  annot1,
  annot2,
  bin_width = 10,
  plot_title,
  x_label,
  y_label,
  legend_facet_label,
  legend_cum_label,
  quiet = FALSE
)

Arguments

annotated_regions	A GRanges returned from annotate_regions().
x	A string indicating the column of the GRanges to use for the x-axis.
y	A string indicating the column of the GRanges to use for the y-axis. If missing, a histogram over x will be plotted. If not missing, a scatterplot is plotted.
annot1	A string indicating the first annotation type.
annot2	A string indicating the second annotation type.
bin_width	An integer indicating the bin width of the histogram used for score. Default 10. Select something appropriate for the data. NOTE: This is only used if y is NULL.
plot_title	A string used for the title of the plot. If missing, no title is displayed.
x_label	A string used for the x-axis label. If missing, no x-axis label is displayed.
y_label	A string used for the y-axis label. If missing, no y-axis label is displayed.
legend_facet_label	A string used to label the gray bar portion of the legend. Defaults to "x in annot pair".
legend_cum_label	A string used to label the red outline portion of the legend. Defaults to "All x".
quiet	Print progress messages (FALSE) or not (TRUE).

Details

For example, a CpG with associated percent methylation annotated to a CpG island and a promoter will count once in the All distribution and once in the CpG island / promoter facet distribution. However, a CpG associated only with a promoter will count once in the All distribution and once in the promoter / promoter distribution.

Value

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

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)

   dm_vs_num_co = plot_numerical_coannotations(
       annotated_regions = dm_annots,
       x = 'mu0',
       annot1 = 'hg19_cpg_islands',
       annot2 = 'hg19_cpg_shelves',
       bin_width = 5,
       plot_title = 'Group 0 Perc. Meth. in CpG Islands and Promoters',
       x_label = 'Percent Methylation')

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