plot_categorical {annotatr} | R Documentation

## Plot a categorical data variable over another

### Description

Given a `GRanges` of annotated regions from `annotate_regions()`, visualize the the distribution of categorical data `fill` in categorical data `x`. A bar representing the distribution of all `fill` in `x` will be added according to the contents of `fill`. This is the distribution over all values of `x`. Additionally, when `annotated_random` is not missing, a "Random Regions" bar shows the distribution of random regions over `fill`.

### Usage

    plot_categorical(annotated_regions, annotated_random, x, fill = NULL,
      x_order = NULL, fill_order = NULL, position = "stack", plot_title,
      legend_title, x_label, y_label, quiet = FALSE)

### Arguments

`annotated_regions` | The `GRanges` result of `annotate_regions()`.
`annotated_random` | The `GRanges` result of `annotate_regions()` on the randomized regions created from `randomize_regions()`. Random regions can only be used with `fill == 'annot.type'`.
`x` | One of 'annot.type' or a categorical data column, indicating whether annotation classes or data classes will appear on the x-axis.
`fill` | One of 'annot.type', a categorical data column, or `NULL`, indicating whether annotation classes or data classes will fill the bars. If `NULL` then the bars will be the total counts of the x classes.
`x_order` | A character vector that subsets and orders the x classes. Default `NULL`, uses existing values.
`fill_order` | A character vector that subsets and orders the fill classes. Default `NULL`, uses existing values.
`position` | A string which has the same possible values as in `ggplot2::geom_bar(..., position)`, i.e., 'stack', 'fill', 'dodge', etc.
`plot_title` | A string used for the title of the plot. If missing, no title is displayed.
`legend_title` | A string used for the legend title to describe fills (if fill is not `NULL`). Default displays corresponding variable name.
`x_label` | A string used for the x-axis label. If missing, corresponding variable name used.
`y_label` | A string used for the y-axis label. If missing, corresponding variable name used.
`quiet` | Print progress messages (FALSE) or not (TRUE).

### Details

For example, if a differentially methylated region has the categorical label hyper, and is annotated to a promoter, a 5UTR, two exons, and an intron. Each annotation will appear in the All bar once. Likewise for the hyper bar if the differential methylation status is chosen as `x` with `annot.type` chosen as `fill`.

### 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, genome = 'hg19',
           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_order = c(
           'hyper',
           'hypo')
       cpg_order = c(
           'hg19_cpg_islands',
           'hg19_cpg_shores',
           'hg19_cpg_shelves',
           'hg19_cpg_inter')

       dm_vn = plot_categorical(
           annotated_regions = dm_annots,
           x = 'DM_status',
           fill = 'annot.type',
           x_order = dm_order,
           fill_order = cpg_order,
           position = 'fill',
           legend_title = 'knownGene Annotations',
           x_label = 'DM status',
           y_label = 'Proportion')

       # Create randomized regions
       dm_rnd_regions = randomize_regions(regions = dm_regions)
       dm_rnd_annots = annotate_regions(
           regions = dm_rnd_regions,
           annotations = annotations,
           ignore.strand = TRUE)

       dm_vn_rnd = plot_categorical(
           annotated_regions = dm_annots,
           annotated_random = dm_rnd_annots,
           x = 'DM_status',
           fill = 'annot.type',
           x_order = dm_order,
           fill_order = cpg_order,
           position = 'fill',
           legend_title = 'knownGene Annotations',
           x_label = 'DM status',
           y_label = 'Proportion')

[Package annotatr version 1.4.1 Index]