plot_numerical_coannotations: Plot numerical data occurring in pairs of annotations

Description Usage Arguments Details Value Examples

View source: R/visualize.R

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

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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

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   # 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 June 30, 2018, 4:10 p.m.