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micropan (version 1.1.2)

plot.Panmat: Plot and summary of Panmat objects

Description

Generic functions for plotting and printing the content of a Panmat object.

Usage

"plot"(x, col = "black", xlab = "Number of genomes", ylab = "Number of clusters", ...)
"summary"(object, ...)

Arguments

x
A Panmat object, see below.
col
The color, default is "black", of interior and borders of the bars in the barplot.
xlab
The label of the X axis.
ylab
The label of the Y axis.
object
A Panmat object, see below.
...
Optional (graphical) arguments.

Details

A Panmat object contains a pan-matrix, which is the fundamental data structure for pan-genome analyses. It is a small (S3) extension to a matrix. It has one row for each genome in the study, and one column for each gene cluster. The number in cell [i,j] is the number of sequences in genome i that belongs to cluster j. A Panmat object is typically created by the function panMatrix.

The plot.Panmat function will display the content of the Panmat object as a bar chart showing the number of clusters found in 1,2,...,G genomes, where G is the total number of genomes in the study (rows in Panmat).

The summary.Panmat function will display a text giving the same information as plot.Panmat.

See Also

panMatrix.

Examples

Run this code
# See examples in the Help-file for panMatrix.

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