regionplot: Regional association plot

In tobyjohnson/gtx: Genetics ToolboX

Description

Draw regional association plot.

Usage

regionplot(analysis,
           chrom, pos_start, pos_end, pos, 
           hgncid, ensemblid, rs,
           surround = 500000,
           entity, 
           style = 'signals', 
           protein_coding_only = TRUE,
           maf_ge, rsq_ge, 
           emac_ge, case_emac_ge,
           dbc = getOption("gtx.dbConnection", NULL))
regionplot.data(analysis,
                chrom, pos_start, pos_end, pos, 
                hgncid, ensemblid, rs, surround = 500000,
                entity, 
                style = 'signals',
                maf_ge, rsq_ge, 
                dbc = getOption("gtx.dbConnection", NULL))
regionplot.region(chrom, pos_start, pos_end,
                  hgncid, ensemblid, surround = 500000, 
                  dbc = getOption("gtx.dbConnection", NULL))
regionplot.new(chrom, pos_start, pos_end,
               hgncid, ensemblid, surround = 500000, 
               pmin = 1e-10,
	       protein_coding_only = TRUE,   
               dbc = getOption("gtx.dbConnection", NULL))
regionplot.genelayout(chrom, pos_start, pos_end,
                      ymax, cex = 0.75, 
		      protein_coding_only = TRUE, 
                      dbc = getOption("gtx.dbConnection", NULL))
regionplot.genedraw(gl)
regionplot.points(pos, pval,
                  pch = 21,
                  bg = rgb(.67, .67, .67, .5),
                  col = rgb(.33, .33, .33, .5),
                  cex = 1, 
                  suppressWarning = FALSE)
regionplot.recombination(chrom, pos_start, pos_end,
                         yoff = -.5, 
                         dbc = getOption("gtx.dbConnection", NULL))

Arguments

analysis	The key value for the GWAS analysis to plot results from
chrom	Character specifying chromosome
pos_start	Start position of region
pos_end	End position of region
pos	Position to define region around
hgncid	HGNC identifier of gene to define region around
ensemblid	ENSEMBL gene identifier to define region around
rs	dbSNP rs identifier of variant to define region around
surround	Distance around gene to include in region
entity	Entity, as ENSEMBL or HGNC id, of entity within eQTL data to plot results for
style	Character specifying plot style
protein_coding_only	Whether to restrict annotation to protein coding genes only
maf_ge	Filtering threshold, minor allele frequency greater-or-equal than
rsq_ge	Filtering threshold, imputation r-squared greater-or-equal than
emac_ge	Filtering threshold, minor allele count greater-or-equal than
case_emac_ge	Filtering threshold, case minor allele count greater-or-equal than
pmin	Smallest P-value to size plot region for
ymax	Largest y-axis value to plan gene layout for
cex	Relative size for gene name labels
gl	Object returned by regionplot.genelayout
yoff	Y axis offset for baseline of recombination rate
dbc	Database connection

Details

The highest level function, regionplot, draws a regional association plot, by querying the required data via a database connection (see gtxdbcheck). Some lower level functions provide component parts to assist in generating modified plots (e.g. multiple analysis results in the same plot, or user specified plot colours or symbols).

The region to plot results over can be specified in several different ways. The region can be supplied as physical coordinates using the arguments chrom, pos_start and pos_end. Alternatively, the region can be centered on a gene of interest, using either the hgncid or emsemblid argument, and the size of region around the gene can be modified using the surround argument.

Value

regionplot returns an invisible null. The plot is generated as a side effect.

Author(s)

Toby Johnson [e-mail]

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.