phyclust (version 0.1-9)

plotgaps: Gaps plots of sequences for visual comparisons

Description

This function provides gaps plots of data set to identify regions where gaps enriched. The plot show the proportions of context by sites and the diverse may be caused by mutations, sequencing errors, or alignment errors.

Usage

plotgaps(X, code.type = .code.type[1], main = "Gaps Plot",
    xlab = "Sites", ylab = "Proportion", ...)

Arguments

X

numerical data matrix with $N$ rows/sequences and $L$ columns/sites.

code.type

either "NUCLEOTIDE" (default) or "SNP".

main

main label, default = "Gaps Plot".

xlab

x-axis label, default = "Sites".

ylab

y-axis label, default = "Proportion".

...

other options passed to plot.

Value

• A gaps plot will be drawn.

Details

Proportions of gaps will be drawn.

References

Phylogenetic Clustering Website: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

See Also

plotdots.

Examples

# For nucleotide
set.seed(1234)
X <- seq.data.toy$org
X[sample(c(T, F), length(X), replace = TRUE, prob = c(0.05, 0.95))] <-
  .nucleotide$nid[.nucleotide$code == "-"]
plotgaps(X)