extractCoord: A function to extract plotting coordinates, either for...

In RCM: Fit row-column association models with the negative binomial distribution for the microbiome

Description

A function to extract plotting coordinates, either for plot.RCM or to export to other plotting software

Usage

extractCoord(RCM, Dim = c(1, 2))

Arguments

RCM

an RCm object

Dim

an integer vector of required dimensions The parameters for the ellipses of the quadratic response function come from the parametrization f(x) = a*x^2 + b*x + c For an unconstrained object the row and column coordinates are returned in separate matrices. The row names will correspond to the labels. For a constrained analysis also the variable points are returned. All variables still need to be scaled to optimally fill the available space

Value

A list with components

samples	A dataframe of sample scores
species	A dataframe of column scores, with origin, slope, end and ellipse coordinates as needed
variables	A dataframe of variable scores, loadings of the environmental gradient

Examples

data(Zeller)
require(phyloseq)
tmpPhy = prune_taxa(taxa_names(Zeller)[1:100],
prune_samples(sample_names(Zeller)[1:50], Zeller))
zellerRCM = RCM(tmpPhy, k = 2, round = TRUE)
coordsZeller = extractCoord(zellerRCM)

RCM documentation built on Nov. 8, 2020, 5:22 p.m.