snpEnrichment (version 1.7.0)

plot-methods: Plot method (S4) for Enrichment object

Description

plot is a generic function for plotting of R objects. The function invokes particular methods which depend on the class of the first argument.

Usage

"plot"(x, what = "Genome", type = c("eSNP", "xSNP"), ggplot = FALSE, pvalue = TRUE, ...)

Arguments

x

[Enrichment]: an object of class Enrichment which the Z statistics or p-values have to be drawn.

what

[character or vector(numeric)]: default what="Genome") plot Z statistics or p-values for genome only (what must be: "All", "Genome" or numeric vector).

type

[vector(character)]: plot the selected analysis for "eSNP" and/or "xSNP".

ggplot

[logical]: use ggplot (default ggplot=FALSE) instead of classic plot method.

pvalue

[logical]: if TRUE, p-value convergense is plotted. Otherwise, Z statistic is plotted.

...

[any]: Arguments to be passed to methods, such as graphical parameters (see par)

See Also

Overview : snpEnrichment-package Classes : Enrichment, Chromosome, EnrichSNP Methods : plot, reSample, getEnrichSNP, excludeSNP, compareEnrichment, enrichment, is.enrichment, chromosome, is.chromosome Functions : initFiles, writeLD, readEnrichment

Examples

## Not run: data(toyEnrichment)
# reSample(toyEnrichment, 10)
# plot(toyEnrichment)## End(Not run)