R: Plot Ancestry Proportions

snpgdsAdmixPlot {SNPRelate}

R Documentation

Plot Ancestry Proportions

Description

Plot the admixture proportions according to their ancestries.

Usage

snpgdsAdmixPlot(propmat, group=NULL, col=NULL, multiplot=TRUE, showgrp=TRUE,
    shownum=TRUE, ylim=TRUE, na.rm=TRUE)
snpgdsAdmixTable(propmat, group, sort=FALSE)

Arguments

`propmat`	a sample-by-ancestry matrix of proportion estimates, returned from `snpgdsAdmixProp()`
`group`	a character vector of a factor according to the samples in `propmat`
`col`	specify colors
`multiplot`	single plot or multiple plots
`showgrp`	show group names in the plot
`shownum`	`TRUE`: show the number of each group in the figure
`ylim`	`TRUE`: y-axis is limited to [0, 1]; `FALSE`: `ylim <- range(propmat)`; a 2-length numeric vector: `ylim` used in `plot()`
`na.rm`	`TRUE`: remove the sample(s) according to the missing value(s) in `group`
`sort`	`TRUE`: rearranges the rows of proportion matrices into descending order

Details

The minor allele frequency and missing rate for each SNP passed in snp.id are calculated over all the samples in sample.id.

Value

snpgdsAdmixPlot(): none.

snpgdsAdmixTable(): a list of data.frame consisting of group, num, mean, sd, min, max

Author(s)

Xiuwen Zheng

References

Zheng X, Weir BS. Eigenanalysis on SNP Data with an Interpretation of Identity by Descent. Theoretical Population Biology. 2015 Oct 23. pii: S0040-5809(15)00089-1. doi: 10.1016/j.tpb.2015.09.004.

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

# get population information
#   or pop_code <- scan("pop.txt", what=character())
#   if it is stored in a text file "pop.txt"
pop_code <- read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))

# get sample id
samp.id <- read.gdsn(index.gdsn(genofile, "sample.id"))

# run eigen-analysis
RV <- snpgdsEIGMIX(genofile)

# define groups
groups <- list(CEU = samp.id[pop_code == "CEU"],
    YRI = samp.id[pop_code == "YRI"],
    CHB = samp.id[is.element(pop_code, c("HCB", "JPT"))])

prop <- snpgdsAdmixProp(RV, groups=groups)

# draw
snpgdsAdmixPlot(prop, group=pop_code)

# close the genotype file
snpgdsClose(genofile)

[Package SNPRelate version 1.10.2 Index]