plot_region_data: Plot statistics in a particular region

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

Description

This is a function to plot statistics on a particular scaffold or chromosome, or in a particular region of that scaffold or chromosome. The input may be 1) the raw tibble from any of the loading functions, 2) a reordered tibble, or 3) a tibble with cumulative positions. This function will operate differently on each of these input types. If the input already has cumulative positions (i.e. column bp_cum), then the "from" and "to" variables are interpreted as "from = bp_cum start" and "to = bp_cum end". If the input does not have column bp_cum, then this function will generate bp_cum according to the desired chromosome or scaffold, assume that the supplied "from" and "to" arguments are scaffold positions, and determine the appropriate "from" and "to" coordinates from the new bp_cum coordinates. You may only specify a chromosome OR a scaffold.

Usage

plot_region_data(input, chromosome = NA, scaffold = NA, from = 1,
  to = NA, type = "gwas", color = "black",
  plotting_column = "stat", scaffold_lengths, include_all_p = FALSE)

Arguments

input	A tibble with four named columns (scaf, ps, stat, and chr)
chromosome	Chromosome to plot. This OR scaffold may be specified.
scaffold	Scaffold to plot. This OR chromosome may be specified.
from	Start position, if desired.
to	End position, if desired
type	Type of statistic: gwas, popgen.
color	Color for points.
plotting_column	Name of the column to plot. Usually will be 'stat'
scaffold_lengths	Path to a two-column tab delimited file with scaffold and length.
include_all_p	Plot p-values <0.05?

Value

A ggplot.

Examples

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

b <- load_gemma_gwas( a1, pval = 'p_wald' )
chrom <- b$chr[ b$scaf == "scaffold_1000" ][1]

c <- plot_region_data( b, chromosome = chrom, type = 'gwas',
plotting_column = 'stat', scaffold_lengths = a2)
c

nwvankuren/gwplotting documentation built on April 17, 2021, 2:37 p.m.