plotEFF: plotEFF

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

plotEFF

Description

plotEFF

Usage

plotEFF(
  siteEFF,
  gff = gff,
  Chr = Chr,
  start = start,
  end = end,
  showType = c("five_prime_UTR", "CDS", "three_prime_UTR"),
  CDS.height = CDS.height,
  cex = 0.1,
  col = c("red", "yellow"),
  pch = 20,
  main = main,
  legend.cex = 0.8,
  gene.legend = TRUE,
  markMutants = TRUE,
  mutants.col = 1,
  mutants.type = 1,
  y = c("pvalue", "effect"),
  ylab = ylab,
  legendtitle = legendtitle,
  par.restore = TRUE
)

Arguments

siteEFF	matrix, column name are pheno names and row name are site position
gff	gff annotation
Chr	the chromosome name
start	start position
end	end position
showType	character vector, eg.: "CDS", "five_prime_UTR", "three_prime_UTR"
CDS.height	numeric indicate the height of CDS in gene model, range: ⁠[0,1]⁠
cex	a numeric control the size of point
col	vector specified the color bar
pch	vector controls points type, see par()
main	main title
legend.cex	a numeric control the legend size
gene.legend	whether add legend for gene model
markMutants	whether mark mutants on gene model, default as TRUE
mutants.col	color of lines which mark mutants
mutants.type	a vector of line types
y, ylab, legendtitle	y: indicate either pvalue or effect should be used as y axix, ylab,legendtitle:,character, if missing, the value will be decide by y.
par.restore	default as TRUE, wether restore the origin par after ploted EFF.

Value

No return value, called for side effects

Examples

data("geneHapR_test")

# calculate site functional effect
# siteEFF <- siteEFF(hapResult, pheno, names(pheno))
# plotEFF(siteEFF, gff = gff, Chr = "scaffold_1")

geneHapR documentation built on May 29, 2024, 11:59 a.m.