Plotting haplotype accumulation curves

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Description

Plots the accumulation curves calculated by haploAccum.

Usage

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## S3 method for class 'haploAccum'
plot(x, add = FALSE, ci = 2, ci.type = c("bar","line","polygon"), 
    col = par("fg"), ci.col = col, ci.lty = 1, xlab, ylab = "Haplotypes", ylim,  
    main = paste(x$method, "method of haplotype accumulation", sep=" "), ...)

Arguments

x

A ‘haploAccum’ object obtained from haploAccum.

add

Add graph to an existing graph.

ci

Multiplier for the calculation of confidence intervals from standard deviation. ci = 0 prevents the drawing of confidence intervals.

ci.type

Type of confidence intervals: "bar" for vertical bars, "line" for lines, and "polygon" for a shaded area.

col

Colour for curve line.

ci.col

Colour for lines or shaded area when "polygon".

ci.lty

Line type for confidence interval lines or border of the "polygon".

xlab

Label for the X-axis.

ylab

Label for the Y-axis.

ylim

Y-axis limits.

main

Title of the plot.

...

Other parameters to pass to plot.

Value

Plots a haplotype accumulation curve and confidence intervals depending on the options given to haploAccum.

Author(s)

Jagoba Malumbres-Olarte <j.malumbres.olarte@gmail.com>.

References

Gotellli, N.J. & Colwell, R.K. (2001). Quantifying biodiversity: procedures and pitfalls in measurement and comparison of species richness. _Ecology Letters_ *4* 379–391.

Examples

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data(dolomedes)
#Generate multiple haplotypes
doloHaplo <- dolomedes[sample(37, size = 200, replace = TRUE), ] 
dolocurv <- haploAccum(doloHaplo, method = "random", permutations = 100)

plot(dolocurv)
plot(dolocurv, add = FALSE, ci = 2, ci.type = "polygon", col = "blue", ci.col = "red", 
    ci.lty = 1)

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