make_locuszoom: Make a locuszoom plot. Details see http://locuszoom.org/.

In boxiangliu/locuscomparer: locuscomparer: Visualization of GWAS-QTL Colocalization Events

Make a locuszoom plot. Details see http://locuszoom.org/.

Description

Make a locuszoom plot. Details see http://locuszoom.org/.

Usage

make_locuszoom(metal, title, chr, color, shape, size,
  ylab_linebreak = FALSE)

Arguments

metal	(data.frame) input file with two column, rsID and p-value. See 'read_metal()' for more details.
title	(string) y-axis title.
chr	(string) chromosome.
color	(data.frame) The output from 'assign_color()'.
shape	(data.frame) Specification of the shape of each SNP. See example blow on how to generate this data.frame.
size	(data.frame) Specification of the size of each SNP. See example below on how to generate this data.frame.
ylab_linebreak	(boolean, optional) Whether to break the line of y-axis. If FALSE, the y-axis title and '-log10(p-value)' will be on the same line. Default: FALSE.

Examples

# The data.frame `d1` comes from the example of `read_metal()`,
# The data.frame `color` comes from the example of `assign_color()`.
snp = 'rs9349379'
shape = ifelse(merged$rsid == snp, 23, 21)
names(shape) = merged$rsid
size = ifelse(merged$rsid == snp, 3, 2)
names(size) = merged$rsid
chr = '6'
make_locuszoom(d1, title = 'GWAS', chr, color, shape, size)

boxiangliu/locuscomparer documentation built on Nov. 27, 2022, 7:26 a.m.