propr: The propr Package

Description

Welcome to the propr package!

To learn more about how to calculate metrics of proportionality, see the help file for the method definitions phit and perb.

To learn more about the resultant propr class object, see the help file for the class definition propr-class.

To learn more about compositional data analysis, and its relevance to biological count data, see the attached vignette.

To learn more about propr class methods, see below.

Usage

"show"(object)
"subset"(x, subset, select)
"["(x, i, j, drop)
"$"(x, name)
"plot"(x, y, title = "Pairwise Proportionality")
"image"(x, cexRow = 10, cexCol = 10, title = "*LR Transformed Image")
dendrogram(object, title = "Proportional Clusters", group)

Arguments

object, x

An object of class propr.

subset

Subsets via object@counts[subset, ]. Use this argument to rearrange subject order.

select

Subsets via object@counts[, select]. Use this argument to rearrange feature order.

i, j, drop

Subsets via object@pairs[i, j, drop].

name

Subsets via object@pairs[, name].

Missing. Ignore. Leftover from the generic method definition.

title

A character string. A title for the propr plot.

cexRow

Numeric. Size of x-axis label.

cexCol

Numeric. Size of y-axis label.

group

A character or numeric vector. Supply feature groups for coloring. Feature groups expected in the order they appear in @counts.

Methods (by generic)

show: Method to show propr object. subset: Method to subset propr object. [: Method to subset propr object. $: Method to subset propr object. plot: Method to plot propr object. image: Method to plot propr object. plot: Method to plot propr object.