ggmanZoom: ggmanZoom

Description Usage Arguments Value Examples

View source: R/ggmanZoom.R

Description

Zoom in to a specific region of the Manhattan Plot

Usage

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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

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#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 Oct. 17, 2018, 2:25 a.m.