plot_gwas: Plot annotated manhattan plot

In Gregor-Mendel-Institute/gwaR: A collection of R functions to conduct GWAS analysis (in Arabidopsis thaliana)

Plot annotated manhattan plot

Description

Plot annotated manhattan plot

Usage

plot_gwas(
  gwas_table,
  title = "No Title",
  subtitle = NULL,
  p_filter = 2,
  mac_filter = 0,
  nlabels = 5,
  annotated = TRUE,
  labeltype = "GeneId",
  match_nearest = FALSE
)

Arguments

gwas_table	Object returned from format_gwas function
title	Specify plot title
subtitle	Specify plot subtitle
p_filter	everything with a log10(p) below this value will not be included in the plot (default: 2)
mac_filter	everything with a mac (minor allele count) below this will not be plotted. (default: 0)
nlabels	How many labels should be plotted (default: 5)
annotated	Should the plot contain annotations for some peaks (controls see below)? Default is TRUE
labeltype	Which entry from the lookup should be displayed (character, defaults to "GeneId"). Options: SNP_rank, chrom, pos, Significant, log10_p, mac, GeneId, max_distance, description, transcript_biotype, start_position, end_position.
match_nearest	Defaults to FALSE; if TRUE will use find_nearest_genes instead of find_overlapping_genes for annotations

Details

Based on a GWAS table, generates a manhatten plot, with gene annotations. Number of annotations can be toggled by changing nlabels. By default only plots annotations for SNPs that are within a gene annotation. For performance reasons, everything with a log10(p) smaller than p_filter is filtered out.

See Also

format_gwas

plot_gwas

get_nearest_genes

get_overlapping_genes

Gregor-Mendel-Institute/gwaR documentation built on Feb. 8, 2023, 8:34 p.m.