propr (version 3.1.8)

propr: The propr Package

Description

Welcome to the propr package!

To learn more about calculating proportionality, see proportionality.

To learn more about visualizing proportionality, see visualize.

To learn more about ALDEx2 package integration, see aldex2propr.

To learn more about differential proportionality, see propd.

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

Usage

# S4 method for propr
show(object)
# S4 method for propr
subset(x, subset, select)
# S4 method for propr,ANY,ANY
[(x, i = "all", j, tiny = FALSE)
# S4 method for propr,missing
plot(x, y, prompt = TRUE, plotly = FALSE)
simplify(object)
adjacent(object)

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

Operation used for the subset indexing. Select from "==", "=", ">", ">=", "<", "<=", "!=", or "all".

j

Reference used for the subset indexing. Provide a numeric value to which to compare the proportionality measures in the @matrix slot.

tiny

A logical scalar. Toggles whether to pass the indexed result through simplify.

y

Missing. Ignore. Leftover from the generic method definition.

prompt

A logical scalar. Set to FALSE to disable the courtesy prompt when working with big data.

plotly

A logical scalar. Set to TRUE to produce a dynamic plot using the plotly package.

Slots

counts

A matrix. Stores the original "count matrix" input.

logratio

A matrix. Stores the log-ratio transformed "count matrix".

matrix

A matrix. Stores the proportionality matrix calculated by phiRcpp or rhoRcpp.

pairs

A vector. Indexes the proportionality metrics of interest.

Methods (by generic)

show: Method to show propr object.

subset: Method to subset propr object.

[: Method to subset propr object.

plot: Method to plot propr object.

Functions

simplify: This convenience function takes an indexed propr object and subsets the object based on that index. Then, it populates the @pairs slot of the new object with an updated version of the original index. You can call simplify from within the [ method using the argument tiny.

adjacent: This function uses pairs indexed in the @pairs slot to build a symmetric adjacency matrix.