jimmyodonnell

library(geosphere)

# First, pick a starting point for one of the transects.
start.point.1 <- matrix(data = c(-122.54727, 47.57078), nrow=1)

# Set two other starting points, 1000 meters from the first, in opposite directions
start.point.2 <- destPoint(start.point.1, 30, 1000)
start.point.3 <- destPoint(start.point.1, 210, 1000)

# Pick the distances along each transect you want to sample

jimmyodonnell

# sample structure plots
# to suppress axis ticks, use:
# xaxt = "n", yaxt = "n"
# no borders lty=0 or border=0
par(mfcol=c(4,2), mar=c(2,2,1,1), oma=c(2,4,2,2))

plot(0,1,type="n", ylim=c(0,1), xlim=c(0,100), xlab=NA, ylab=NA, yaxp  = c(0, 1, 2))
rect(0,0,100,1, col="yellow", border=0)

plot(0,1,type="n", ylim=c(0,1), xlim=c(0,100), xlab=NA, ylab=NA, yaxp  = c(0, 1, 2))

jimmyodonnell

# For any two DNA sequences, this code will generate a single sequence which represents differences among them with the IUPAC ambiguities.

het.cbm <- function(x1, x2){
	if (length(x1)!=length(x2)) stop("sequences are not the same length!")
	oot <- paste(x1, x2, sep="")
# define nucleotides
	nucleotides<-c("A", "C", "G", "T")

# make a matrix of all possible combinations of nucleotides
	combos <- matrix(NA, 4,4)