ggmanZoom: ggmanZoom

In veera-dr/ggman: R package for Manhattan Plots

Description

Zoom in to a specific region of the Manhattan Plot

Usage

ggmanZoom(ggmanPlot, chromosome, start.position = NA, end.position = NA,
  gene.tracks = TRUE, ymax = 10, genome = "hg19", exon.width = 0.5,
  gene.width = 0.05, stack.level = 1, remove.gene.text.overlap = FALSE,
  gene.text.size = 2, xlabel = NA, ylabel = NA, title = NA, ...)

Arguments

ggmanPlot	A ggplot object of class 'ggman'
chromosome	Chromosome identifier
start.position	Starting basepair position
end.position	Ending basepair position
gene.tracks	if TRUE, refseq gene tracks will be downloaded frm UCSC server and plotted. default is TRUE
ymax	maximum limit of y axis
genome	genome build version; default is 'hg19'
exon.width	width of the exons in the gene tracts; default is 0.5
gene.width	with of the introns in the gene tracts; default is 0.05
stack.level	levels of stacking of the gene tracts; default is 1, where all the genes are plotted in single track
remove.gene.text.overlap	if TRUE, one of the overlapping gene text labels will be removed
gene.text.size	size of gene labes below the gene tracts; default is 2
xlabel	X axis label
ylabel	Y axis label
title	Plot title
...	other arguments to pass to geom_point

Value

A regional association plot

Examples

#specific chromosome
p1 <- ggman(toy.gwas, snp = "snp", bp = "bp", chrom = "chrom",
pvalue = "pvalue")
ggmanZoom(p1, chromosome = 1)

#specific region
ggmanZoom(p1, chromosome = 1, start.position = 215388741, end.position = 238580695)

veera-dr/ggman documentation built on May 3, 2019, 4:59 p.m.