displayVarOnGeneModel {geneHapR}

Display Variants on Gene Model

Description

show variants on gene model using hapSummary and gene annotations

Usage

displayVarOnGeneModel(
  hapSummary,
  gff,
  Chr,
  startPOS,
  endPOS,
  type = "pin",
  cex = 0.7,
  CDS_h = 0.05,
  fiveUTR_h = 0.02,
  threeUTR_h = 0.01,
  geneElement = geneElement,
  hap
)

Arguments

hapSummary, hap

haplotype result

gff

gff

Chr

the chromosome name. If missing, the first element in the hapSummary will be used

startPOS

If missing, will use the min position in hapSummary

endPOS

If missing, will use the max position in hapSummary

type

character. Could be "circle", "pie", "pin", "pie.stack" or "flag"

cex

a numeric control the size of circle

CDS_h, fiveUTR_h, threeUTR_h

The height of CDS 5'UTR and 3'UTR in gene model

geneElement

ploted elements, eg.: c("CDS","five_prime_UTR")

Value

No return value

Examples

data("geneHapR_test")
hapSummary <- hap_summary(hapResult)
displayVarOnGeneModel(hapSummary, gff,
                      startPOS = 4100,
                      endPOS = 8210,
                      cex = 0.75)