plot.sgsObj: Plot spatial locations of individuals in sgsObj data...

In lukembrowne/sgsR: Spatial genetic structure analyses in R

Description

Plot spatial locations of individuals in sgsObj data structure

Usage

## S3 method for class 'sgsObj'
plot(x, pch = 19, ...)

Arguments

x	An sgsObj data structure to be plotted
pch	Type of plotting character to display
...	Any arguments to pass to the generic plot function

Value

Plots the spatial location of individuals in the sgsObj data structure.

Examples

## Simulate genetic data
Nind = 100 # Number of individuals
Nloci = 5 # Number of loci
Nallele = 10 # Number of alleles per loci

## Set up data frame and generate random spatial locations
dat <- data.frame(id = 0:(Nind - 1))
dat$x = runif(Nind, 0, 100)
dat$y = runif(Nind, 0, 100)

## Simulate Random genetic data and assign loci names
for (loci in 1:Nloci) {
 loci_name_a = paste("Loc", loci, "_A", sep = "")
 loci_name_b = paste("Loc", loci, "_B", sep = "")
 dat[loci_name_a] <- sample.int(Nallele, Nind, replace = TRUE)
 dat[loci_name_b] <- sample.int(Nallele, Nind, replace = TRUE)
}

## Convert to sgsObj
sgsObj = createSgsObj(sample_ids = dat$id,
                     genotype_data = dat[, 4:(Nloci*2 + 3)],
                     ploidy = 2,
                     x_coords = dat$x,
                     y_coords = dat$y,
                     missing_val = -999)

summary(sgsObj)

plot(sgsObj)

plot(sgsObj, pch = 21, col = "steelblue", cex = 1.5)

lukembrowne/sgsR documentation built on May 21, 2019, 8:58 a.m.