add_annotations: Create a tibble containing information for plotting gene...

In nwvankuren/gwplotting: Utilities for plotting statistics from genome-wide analyses

Create a tibble containing information for plotting gene models using ggplot and geom_rect().

Description

This function will calculate the coordinates of scaffold spans or gene models for addition to a ggplot. It will use scaffold spans encoded in the input tibble. GFF features of the specified type will be plotted if a GFF file is specified.

Usage

add_annotations(
  input,
  ymin,
  ymax,
  scaffold_lengths,
  gff = NA,
  feature = "gene",
  mapping = "chr"
)

Arguments

input	Tibble containing scaf, ps, stat, chr, and bp_cum ONLY for the region you want to plot. That is, your data has already been reordered.
ymin	Minimum y positions for geom_rects.
ymax	Maximum y positions for geom_rects.
scaffold_lengths	Path to a two-column tab-delimited file containing scaffold names and their lengths.
gff	Path to a GFF or BED format file, if plotting gene models. If left NA, then elements in the output correspond to constituent scaffolds in the plotted region.
feature	GFF feature type to plot. Usually genes. Not extensively tested.
mapping	Path to AGP file, or "chr" if the assembly is already at chromosome level and annotated.

Details

The input must only contain information from the region that you want to plot. The reason for this limitation is that you may want to plot gene models from multiple scaffolds and these will need to be reordered and reoriented based on the scaffold-to-chromosome mapping. You can simply filter in the function call instead of creating another object, though.

Value

A four-column tibble containing an ID, xmins, xmaxs, ymins, and ymaxs for use in a geom_rect() call.

Examples

a1 <- system.file("extdata", "test.gemma_gwas.txt.gz",
                 package = "gwplotting")
a2 <- system.file("extdata", "test.chromSizes.txt.gz",
                  package="gwplotting")

# Load statistics, add cumulative positions (bp_cum)
b <- load_gemma_gwas( a1, pval = 'p_wald' )
c <- get_cumulative_positions( b, scaffold_lengths = a2 )

# Get scaffold rects
scafs <- add_annotations( c, ymin = 0, ymax = 0.5 )

scafs

# Add rects to a plot of the region data
d <- plot_region_data( c, chromosome = 1, type = 'gwas',
                       plotting_column = 'stat', scaffold_lengths = a2) +
     geom_rect( inherit.aes = F,
                data = scafs,
                mapping = aes( xmin = xmins,
                               xmax = xmaxs,
                               ymin = ymins,
                               ymax = ymaxs),
                color = 'black',
                alpha = 0.5,
                size = 0.25 )

d

nwvankuren/gwplotting documentation built on July 5, 2024, 4:24 p.m.