geneHapR (version 1.2.4)

plotEFF: 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
)

Value

No return value, called for side effects

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.

Examples

# \donttest{
data("geneHapR_test")

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