HeatMap: HeatMap

In fst4pg: Genetic Distance Segmentation for Population Genetics

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)                                

fst4pg documentation built on July 4, 2022, 1:06 a.m.