R: Gaps Plots of Sequences for Visual Comparisons

plotgaps {phyclust} | R Documentation

## 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`.

### Details

Proportions of gaps will be drawn.

### Value

A gaps plot will be drawn.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

### See Also

`plotdots`.

### Examples

    ## Not run:
    library(phyclust, quiet = TRUE)

    # 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)

    ## End(Not run)

[Package phyclust version 0.1-30 Index]