extractCoord {RCM} | R Documentation |
A function to extract plotting coordinates, either for plot.RCM or to export to other plotting software
extractCoord(RCM, Dim = c(1, 2))
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 |
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 |
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)