plot.haploAccum {spider} | R Documentation |
Plotting haplotype accumulation curves
Description
Plots the accumulation curves calculated by haploAccum
.
Usage
## 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 |
add |
Add graph to an existing graph. |
ci |
Multiplier for the calculation of confidence intervals from
standard deviation. |
ci.type |
Type of confidence intervals: |
col |
Colour for curve line. |
ci.col |
Colour for lines or shaded area when |
ci.lty |
Line type for confidence interval lines or border of the
|
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
data(dolomedes)
#Generate multiple haplotypes
doloHaplo <- dolomedes[sample(37, size = 200, replace = TRUE), ]
dolocurv <- haploAccum(doloHaplo, method = "random", permutations = 100)
graphics::plot(dolocurv)
graphics::plot(dolocurv, add = FALSE, ci = 2, ci.type = "polygon", col = "blue", ci.col = "red",
ci.lty = 1)