plot_numerical_coannotations {annotatr} | R Documentation |
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.
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)
annotated_regions |
A |
x |
A string indicating the column of the |
y |
A string indicating the column of the |
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 |
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). |
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.
A ggplot
object which can be viewed by calling it, or saved with ggplot2::ggsave
.
# 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')