R: Plot Histogram to Compare Number of Mutations.

plothist {phyclust} | R Documentation

## Plot Histogram to Compare Number of Mutations.

### Description

Plot histogram to compare number of mutations.

### Usage

    plothist(X, X.class = NULL, Mu = NULL, fill.color = .Color,
       draw.all = TRUE, main = "Mutation counts",
       xlab = "Difference", ylab = "Counts", append = FALSE)

### Arguments

`X` | nid/sid matrix with N rows/sequences and L columns/sites.
`X.class` | class ids indicated for all sequences.
`Mu` | a central sequence with length L.
`fill.color` | color to fill the histogram.
`draw.all` | draw a histogram use all sequences.
`main` | main label, default = "Mutation counts".
`xlab` | x-axis label, default = "Difference".
`ylab` | y-axis label, default = "Counts".
`append` | overwrite histograms.

### Details

If `X.class` is set, the histograms will be drawn by classes and all sequences will be compared to the central sequence `Mu`. Otherwise, all sequences will be used to count mutations. `draw.all` is not effect if `X.class` is not set.

If `Mu` is set, it will be used to compare to all other sequences to count mutations. Otherwise, the first sequence of `X` will be used, and the first sequence in the first class will be used if `X.class` is set. If `Mu` is a matrix, the first row will be used as the central sequence.

### Value

Histograms will be drawn to show the number of mutations away from the central sequence.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

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

### See Also

`seqgen`, `plotdots`.

### Examples

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

    X <- seq.data.toy$org
    plothist(X)

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

    ## End(Not run)

[Package phyclust version 0.1-30 Index]