extractCoord {RCM} | R Documentation

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

### 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)

[Package RCM version 1.4.0 Index]