HeatMap {fst4pg}

HeatMap

Description

Make a frequency heatmap

Usage

HeatMap(
  Min,
  Max,
  chr = NULL,
  Info,
  FreqNbG,
  Dir = NULL,
  Weights = NULL,
  Weight.thres = 0.05,
  NbAdjM = 0,
  Subsets = NULL
)

Arguments

Min

the starting position value of the region

Max

the end position value of the region

chr

a string providing the chromosome name, optional

Info

a data.frame providing information about markers

FreqNbG

a list of data.frames (one per population) with two columns: Freq and NbGamete

Dir

a string providing the name of the directory where the graph should be saved, optional

Weights

a vector of weights associated with each marker, optional

Weight.thres

a numeric value. Markers with weights lower than this threshold will be discarded from the graphical representation. Optional.

NbAdjM

an integer providing the number of markers before and after the highlighted regions that should be added to the graphical representation, optional.

Subsets

a list of character vectors with the population names, optional.

Value

A heatmap where rows correspond to markers, and columns to populations.

Examples

## The full example execution takes a few seconds.
# data(Freq);data(NbGamete)
# FreqNbG <- BuildFreqNbG(Freq,NbGamete)
# HFst.m <- HudsonFst.m(FreqNbG)

## Two sets of populations to contrast
# Contrast <- list(America=c("Colombian","Maya"),Europe=c("Tuscan","Italian"))
# Profiles <- HudsonFst.prof(HFst.m,Contrast=Contrast)
# PS <- ProfilingSummary(Profiles,Info) 

# RefLevel <- rapply(Profiles,median,classes = "numeric",how='list')
# Ratio.thres <- 3
# NbSnp.min <- 1
# CS <- ContrastSummary(PS, RefLevel,
#                       Ratio.thres=Ratio.thres,
#                       NbSnp.min=NbSnp.min)
# NbSel.thres <- 2
# TopRegions <- ContrastTopRegions(CS = CS,Crit = 'NbSel',Info = Info,
#                                  Thres = NbSel.thres, Simplify=TRUE)
# HeatMap(Min = TopRegions[1,]$Start,
#         Max = TopRegions[1,]$End,
#         chr = TopRegions[1,]$Chromosome,
#         Info = Info,
#         FreqNbG = FreqNbG,
#         Subsets = Contrast)