R: Dots Plots of Sequences for Visual Comparisons

plotdots {phyclust} | R Documentation

## Dots Plots of Sequences for Visual Comparisons

### Description

This function provides dots plots of data set given an idea how diverse the sequences are by drawing dots with different colors for all mutations.

### Usage

    plotdots(X, X.class = NULL, Mu = NULL, code.type = .code.type[1],
        diff.only = TRUE, fill = FALSE, label = TRUE, with.gap = FALSE,
        xlim = NULL, ylim = NULL, main = "Dots Plot", xlab = "Sites",
        ylab = "Sequences", missing.col = "gray95", ...)

### Arguments

`X` | numerical data matrix with N rows/sequences and L columns/sites.
`X.class` | class ids indicated for all sequences.
`Mu` | a center sequence with length L.
`code.type` | either "NUCLEOTIDE" (default) or "SNP".
`diff.only` | draw the segregating sites only, default = TRUE.
`fill` | fill in all dots, default = FALSE.
`label` | indicate segregating sites, default = TRUE.
`with.gap` | pass to `find.consensus` if `Mu` is `NULL`, default = FALSE
`xlim` | limit of x-axis.
`ylim` | limit of y-axis.
`main` | main label, default = "Dots Plot".
`xlab` | x-axis label, default = "Sites".
`ylab` | y-axis label, default = "Sequences".
`missing.col` | color for the missing allele, default = NA.
`...` | other options passed to `plot`.

### Details

The first rows in `Mu` will be drawn entirely on dots plots in colors which are "green3", "blue2", "\#CC00CC", "red2", "gray", and "white", according the ids + 1. If `fill` is FALSE, other sequences will be drawn by the mutation sites comparing to the first sequences. Otherwise, they be drawn entirely.

If `X.class` is set, the sequences will be drawn in cluster order.

If `Mu` is `NULL`, the consensus sequence of `X` will be drawn.

If `label` is TRUE, the bottom row will be drawn in color "orange" to indicate segregating sites.

`with.gap` is only used when `Mu` is `NULL`.

### Value

A dots plot will be drawn.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

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

### See Also

`seqgen`, `plothist`.

### Examples

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

    # For nucleotide
    X <- seq.data.toy$org
    par(mfrow = c(2, 2))
    plotdots(X)
    plotdots(X, diff.only = FALSE)
    plotdots(X, diff.only = FALSE, label = FALSE)
    plotdots(X, fill = TRUE, diff.only = FALSE, label = FALSE)

    # With class ids
    X.class <- as.numeric(gsub(".*-(.*)", "\\1", seq.data.toy$seqname))
    plotdots(X, X.class)

    # For SNP
    X.SNP <- nid2sid(X)
    plotdots(X.SNP, X.class)

    ## End(Not run)

[Package phyclust version 0.1-30 Index]