plot_fstats: Plot F2, F3, F3star, F4, D or pairwise Fst values with their...

In poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data

Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervals

Description

Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervals

Usage

plot_fstats(
  x,
  stat.name = "F2",
  ci.perc = 95,
  value.range = c(NA, NA),
  pop.sel = NA,
  pop.f3.target = NA,
  highlight.signif = TRUE,
  main = stat.name,
  ...
)

Arguments

x	An object of class fstats (to plot heterozygosities, divergence, F2, F3, F3star, F4 or D statistics) or pairwisefst (to plot pairwise fst)
stat.name	For fstats object, the name of the stat (either heterozygosities, divergence, F2, F3, F3star, F4 or Dstat)
ci.perc	Percentage of the Confidence Interval in number of standard errors (default=95%)
value.range	Range of test values (x-axis) to be plotted (default=NA,NA: i.e., all test values are plotted)
pop.sel	Only plot test values involving these populations (default=NA: i.e., all test values are plotted)
pop.f3.target	For F3-statistics, only plot F3 involving pop.f3.target as a target
highlight.signif	If TRUE highlight significant tests in red (see details)
main	Main title of the plot (default=stat.name)
...	Some other graphical arguments to be passed

Details

Data will only be plotted if jackknife estimates of the estimator s.e. have been performed i.e. if the functions compute.fstats or compute.pairwiseFST were run with nsnp.per.block>0

Value

A plot of the Fstats of interest. Significant F3 statistics (i.e., showing formal evidence for admixture of the target population) are highlighted in red. Significant F4 statistics (i.e., showing formal evidence against treeness of the pop. quadruplet) are highlighted in red.

See Also

To generate x object, see compute.pairwiseFST (for pairwisefst object) or compute.fstats (for fstats object)

Examples

 make.example.files(writing.dir=tempdir())
 pooldata=popsync2pooldata(sync.file=paste0(tempdir(),"/ex.sync.gz"),
                   poolsizes=rep(50,15),poolnames=paste0("P",1:15))
 res.fstats=compute.fstats(pooldata,nsnp.per.bjack.block=25)
 plot_fstats(res.fstats,stat.name="F3",cex=0.5)
 plot_fstats(res.fstats,stat.name="F3",value.range=c(NA,0.001),
             pop.f3.target=c("P7","P5"),cex.axis=0.7)
 plot_fstats(res.fstats,stat.name="F4",cex=0.5) 
 #allow to reduce the size of the test name (y-axis)
 plot_fstats(res.fstats,stat.name="F4",cex=0.5,
             pop.sel=c("P1","P2","P3","P4","P5")) 
 plot_fstats(res.fstats,stat.name="F4",cex=0.5,
             pop.sel=c("P1","P2","P3","P4","P5"),highlight.signif=FALSE)  

poolfstat documentation built on Sept. 8, 2023, 5:49 p.m.