plot.hlaAttrBagObj {HIBAG} | R Documentation

## Plot a HIBAG model

### Description

To show a scatterplot of the numbers of individual classifiers and SNP positions.

### Usage

    ## S3 method for class 'hlaAttrBagObj'
    plot(x, snp.col="gray33", snp.pch=1, snp.sz=1,
        locus.col="blue", locus.lty=1L, locus.lty2=2L, addplot=NULL,
        assembly="auto", ...)
    ## S3 method for class 'hlaAttrBagClass'
    plot(x, ...)

### Arguments

`x` | an object of `hlaAttrBagObj`
`snp.col` | the color of SNP uses
`snp.pch` | the point type of SNP uses
`snp.sz` | the point size of SNP uses
`locus.col` | the color of text and line for HLA locus
`locus.lty` | the type of line for the bounds of HLA locus
`locus.lty2` | the type of line for HLA locus
`addplot` | NULL for creating a plot, or a ggplot object to be appended
`assembly` | the human genome reference: "hg18", "hg19" (default), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning
`...` | further arguments passed to or from other methods

### Value

None

### Author(s)

Xiuwen Zheng

### See Also

`print.hlaAttrBagObj`, `summary.hlaAttrBagObj`

### Examples

    # make a "hlaAlleleClass" object
    hla.id <- "C"
    hla <- hlaAllele(HLA_Type_Table$sample.id,
        H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")],
        H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")],
        locus=hla.id, assembly="hg19")

    # training genotypes
    region <- 100   # kb
    snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position,
        hla.id, region*1000, assembly="hg19")
    train.geno <- hlaGenoSubset(HapMap_CEU_Geno,
        snp.sel = match(snpid, HapMap_CEU_Geno$snp.id))

    # train a HIBAG model
    set.seed(1000)
    # please use "nclassifier=100" when you use HIBAG for real data
    model <- hlaAttrBagging(hla, train.geno, nclassifier=2, verbose.detail=TRUE)
    plot(model)

[Package HIBAG version 1.16.0 Index]