plot_genomewide_data: Plot genome-wide statistics

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

Plot genome-wide statistics

Description

This function will plot the results from genome-wide analyses of diversity, association, etc., that can be generated by a small variety of programs. As of 2019-01, it will handle any tibbles produced by the file_loading_functions. In reality, any tibble containing columns with the names "scaf" (scaffold), "ps" (position on scaffold), "stat" (statistic for plotting), and "chr" (chromosome the scaffold is assigned to, usually a dummy on first load) can be used as input.

Usage

plot_genomewide_data(
  input,
  type = "gwas",
  scaffold_lengths,
  plotting_column = "stat",
  col1 = "grey",
  col2 = "black"
)

Arguments

input	A tibble with four named columns (scaf, ps, stat, and chr)
type	Type of input: gwas, popgen. gwas will -log10 the stat, while popgen will estimate the ylimits.
scaffold_lengths	Name of a two-column tab delimited file containing scaffold and length.
plotting_column	Name of the column to plot. Usually will be 'stat'
col1	Color of odd chromosomes
col2	Color of even chromosomes

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' )

c <- plot_genomewide_data( b, type = 'gwas', scaffold_lengths = a2,
                           plotting_column = 'stat', col1 = 'black',
                           col2 = 'grey' )
c

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