ggmanhattan: Create skeleton of a 'Manhattan plot' (concatenated...

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Create skeleton of a 'Manhattan plot' (concatenated chromosomes) with ggplot2

Usage

ggmanhattan(df, chroms = NULL, scale = c("Mbp", "cM"), space = NULL,
  cols = c("grey30", "grey60"), ...)

Arguments

df	a dataframe with columns (at least) "chr" and "pos"
chroms	chromosome names (in order); will try to guess them if not supplied
scale	one of "Mbp" (millions of basepairs; default) or "cM" (centimorgans)
space	padding factor to add in between chromosomes
cols	vector of length 2, giving alternating colours for alternating chromosomes
...	ignored

Value

a ggplot2 object whose x-axis is defined by chromosome and position (with chromosomes concatenated in karyotype order), to which data in df can be added as additional layers

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.