snpgdsAdmixPlot: Plot Ancestry Proportions

In zhengxwen/SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

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 rows in propmat
col	specify colors; if group is not specified, it is a color for each sample; otherwise specify colors for the groups
multiplot	single plot or multiple plots
showgrp	show group names in the plot; applicable when group is used
shownum	TRUE: show the number of each group on the X-axis in the figure; applicable when group is used
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.

See Also

snpgdsEIGMIX, snpgdsAdmixProp

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, bound=TRUE)

# draw
snpgdsAdmixPlot(prop, group=pop_code)

# use user-defined colors for the groups
snpgdsAdmixPlot(prop, group=pop_code, multiplot=FALSE, col=c(3,2,4))

snpgdsAdmixTable(prop, group=pop_code)

# close the genotype file
snpgdsClose(genofile)

zhengxwen/SNPRelate documentation built on Nov. 19, 2024, 1:02 p.m.