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.

### 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)

    # draw
    snpgdsAdmixPlot(prop, group=pop_code)

    # close the genotype file
    snpgdsClose(genofile)

[Package SNPRelate version 1.26.0 Index]