DEprot.PCoA class

DEprot.PCoA class

Slots

PCoA.metadata

metadata of the samples used in the PCoA (subset of the original DEprot@metadata). Class: "ANY".

sample.subset

vector containing the list of samples analyzed. Class: "ANY".

data.used

vector indicating the type of counts used (imputed, normalized, raw), inherited from the DEprot.correlation object. Class: "ANY".

correlation.method

string indicating the correlation method used to build the dissimilarities ('pearson', 'spearman', 'kendall'). Class: "ANY".

correlation.matrix

the sample-by-sample correlation matrix the PCoA is based on. Class: "ANY".

distance.input

object of class dist as stored in the input DEprot.correlation object, i.e. as.dist(1 - correlation.matrix). Class: "ANY".

distance

object of class dist effectively used for the ordination, after transformation and/or non-euclidean correction. Class: "ANY".

distance.method

string describing how the dissimilarities used were obtained. Class: "ANY".

cmdscale

full output of stats::cmdscale (points, eig, GOF, ac). Class: "ANY".

PCos

data.frame combining the principal coordinates and the metadata table, useful for replotting. Class: "ANY".

eigenvalues

numeric vector of all the eigenvalues returned by the ordination. Class: "ANY".

importance

statistical summary table of the ordination per each principal coordinate (eigenvalue, proportion/percentage of variance, cumulative proportion, broken-stick expectation). Class: "ANY".

euclidean.diagnostics

list summarizing the amount and the magnitude of negative eigenvalues, and the goodness-of-fit of the embedding. Class: "ANY".

axis.loadings

data.frame of protein-vs-axis correlations (only if a DEprot object was provided to perform.PCoA, otherwise NULL). Class: "ANY".

scatter.plot

ggplot object corresponding to the scatter of the two principal coordinates requested by the user. Class: "ANY".

scatter.plot.123

patchwork object combining the PCo1-vs-PCo2 and PCo3-vs-PCo2 scatters. Class: "ANY".

cumulative.PCo.plot

ggplot object showing the proportion of variance and its cumulative curve for each principal coordinate. Class: "ANY".

shepard.plot

ggplot object comparing the input dissimilarities with the distances reconstructed in the reduced space (embedding quality diagnostic). Class: "ANY".

parameters

list of the parameters used to compute the ordination. Class: "ANY".