plot.hlaAttrBagObj: Plot a HIBAG model

In HIBAG: HLA Genotype Imputation with Attribute Bagging

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)

Example output

HIBAG (HLA Genotype Imputation with Attribute Bagging)
Kernel Version: v1.3
Supported by Streaming SIMD Extensions (SSE2) [64-bit]
Build a HIBAG model with 2 individual classifiers:
# of SNPs randomly sampled as candidates for each selection: 10
# of SNPs: 83, # of samples: 60
# of unique HLA alleles: 17
	1  , added snp: 2, loss: 398.296, out-of-bag acc: 40.00%, # of haplo: 16
	2  , added snp: 67, loss: 336.352, out-of-bag acc: 50.00%, # of haplo: 18
	3  , added snp: 37, loss: 276.74, out-of-bag acc: 56.00%, # of haplo: 18
	4  , added snp: 73, loss: 220.983, out-of-bag acc: 64.00%, # of haplo: 18
	5  , added snp: 69, loss: 158.368, out-of-bag acc: 74.00%, # of haplo: 18
	6  , added snp: 40, loss: 133.064, out-of-bag acc: 80.00%, # of haplo: 18
	7  , added snp: 7, loss: 113.799, out-of-bag acc: 82.00%, # of haplo: 18
	8  , added snp: 10, loss: 69.4402, out-of-bag acc: 84.00%, # of haplo: 19
	9  , added snp: 33, loss: 60.9844, out-of-bag acc: 88.00%, # of haplo: 19
	10 , added snp: 43, loss: 60.9816, out-of-bag acc: 90.00%, # of haplo: 19
	11 , added snp: 22, loss: 56.089, out-of-bag acc: 90.00%, # of haplo: 19
	12 , added snp: 5, loss: 49.462, out-of-bag acc: 90.00%, # of haplo: 19
	13 , added snp: 57, loss: 45.5176, out-of-bag acc: 90.00%, # of haplo: 20
	14 , added snp: 83, loss: 42.2249, out-of-bag acc: 90.00%, # of haplo: 24
	15 , added snp: 56, loss: 29.8472, out-of-bag acc: 92.00%, # of haplo: 27
	16 , added snp: 52, loss: 18.2354, out-of-bag acc: 92.00%, # of haplo: 27
	17 , added snp: 27, loss: 12.4665, out-of-bag acc: 92.00%, # of haplo: 27
	18 , added snp: 39, loss: 12.4189, out-of-bag acc: 92.00%, # of haplo: 27
	19 , added snp: 64, loss: 12.3964, out-of-bag acc: 92.00%, # of haplo: 27
	20 , added snp: 20, loss: 12.3785, out-of-bag acc: 92.00%, # of haplo: 27
	21 , added snp: 9, loss: 7.02725, out-of-bag acc: 92.00%, # of haplo: 27
	22 , added snp: 26, loss: 7.01775, out-of-bag acc: 92.00%, # of haplo: 29
	23 , added snp: 34, loss: 7.00894, out-of-bag acc: 92.00%, # of haplo: 29
	24 , added snp: 6, loss: 6.99855, out-of-bag acc: 92.00%, # of haplo: 29
Wed Mar 11 17:28:06 2020,   1 individual classifier, out-of-bag acc: 92.00%, # of SNPs: 24, # of haplo: 29
	1  , added snp: 10, loss: 431.491, out-of-bag acc: 45.00%, # of haplo: 20
	2  , added snp: 44, loss: 366.871, out-of-bag acc: 52.50%, # of haplo: 21
	3  , added snp: 57, loss: 316.627, out-of-bag acc: 67.50%, # of haplo: 23
	4  , added snp: 73, loss: 255.567, out-of-bag acc: 75.00%, # of haplo: 23
	5  , added snp: 34, loss: 210.7, out-of-bag acc: 80.00%, # of haplo: 23
	6  , added snp: 43, loss: 158.083, out-of-bag acc: 85.00%, # of haplo: 23
	7  , added snp: 64, loss: 110.188, out-of-bag acc: 85.00%, # of haplo: 23
	8  , added snp: 3, loss: 104.475, out-of-bag acc: 92.50%, # of haplo: 24
	9  , added snp: 47, loss: 55.7976, out-of-bag acc: 92.50%, # of haplo: 24
	10 , added snp: 49, loss: 55.7638, out-of-bag acc: 95.00%, # of haplo: 24
	11 , added snp: 30, loss: 39.8394, out-of-bag acc: 95.00%, # of haplo: 24
	12 , added snp: 51, loss: 39.6962, out-of-bag acc: 95.00%, # of haplo: 25
	13 , added snp: 75, loss: 31.8408, out-of-bag acc: 95.00%, # of haplo: 29
	14 , added snp: 5, loss: 26.9138, out-of-bag acc: 95.00%, # of haplo: 32
	15 , added snp: 27, loss: 21.6684, out-of-bag acc: 97.50%, # of haplo: 32
	16 , added snp: 32, loss: 21.4032, out-of-bag acc: 97.50%, # of haplo: 32
	17 , added snp: 36, loss: 21.3666, out-of-bag acc: 97.50%, # of haplo: 33
	18 , added snp: 24, loss: 19.2719, out-of-bag acc: 97.50%, # of haplo: 34
Wed Mar 11 17:28:06 2020,   2 individual classifier, out-of-bag acc: 97.50%, # of SNPs: 18, # of haplo: 34

HIBAG documentation built on March 24, 2021, 6 p.m.