manhattan: Fast Manhattan plot for Large Number of P-values

Description Usage Arguments Details Value Note Author(s) See Also Examples

Description

The function manPlotFast creates a Manhattan plot.
The function manPlotPrepare extracts necessary information from a vector of p-values sufficient for creating a Manhattan plot.
It optimized to work quickly even for tens of millions of p-values.

Usage

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manPlotPrepare(
        pvalues,
        chr,
        pos,
        ismlog10 = FALSE,
        chrmargins = 5e6)

manPlotFast(
        man,
        ylim = NULL,
        colorSet = c('steelblue4',"#2C82D1","#4CB2D1"),
        yaxmax = NULL,
        lwd = 3,
        axistep = 2,
        cex = 1)

Arguments

pvalues

Vector of p-values. As is (if ismlog10 = FALSE) or minus log10 transformed (if ismlog10 = TRUE).

chr, pos

Vectors indicating the chromosomes and genomic positions (in basepairs) for each p-value in pvalues.

ismlog10

Specifies whether the provides p-values (pvalues parameter) are minus log10 transformed (- log10(pv))

chrmargins

The plot margins at the ends of chromosomes (in basepairs).

man

Object returned by manPlotPrepare.

ylim

Numeric vectors of length 2, giving the y coordinate range. Exactly as in Plotting Parameters.

colorSet

Colors of points, rotating over chromosomes.
Points for first chromosome have color colorSet[1], next colorSet[2], etc. Once the colors are exhausted, the colors are reused from the beginning.

yaxmax

Maximum reach of the y axis.

lwd

The line width.
As in Graphics Parameters.

axistep

Distance between axis label ticks for y axis.

cex

The size of Manhattan plot points. As in Graphics Parameters.

Details

The function manPlotFast creates Manhattan plot.
It requires the use of the function manPlotPrepare which extracts the necessary information from a vector of p-values sufficient for creating Manhattan plot.
The resulting object is many times smaller than the vector of p-values.

Value

This function manPlotPrepare returns an object with information for creating Manhattan plot.

Note

The plot has no title. To add a title use title.

Author(s)

Andrey A Shabalin [email protected]

See Also

See vignettes: browseVignettes("ramwas").

Examples

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# Simulate data (9 chromosomes, million tests each)
chr = rep(paste0('chr',1:9), each = 1e6)
pos = rep(1:1e6, 9)
pv = runif(9e6)^1.1

# Extract the Manhattan plot info
man = manPlotPrepare(pv, chr, pos, chrmargins = 1000)

# Create Manhattan plot
manPlotFast(man)
title("Manhattan plot")

# Size of p-values before extraction of Manhattan plot info
object.size(list(pv, chr, pos))

# Size of the Manhattan plot info object
object.size(man)

ramwas documentation built on Oct. 31, 2019, 2:11 a.m.