runDPCoA: Calculation of Double Principal Correspondance analysis

In microbiome/mia: Microbiome analysis

Calculation of Double Principal Correspondance analysis

Description

Double Principal Correspondance analysis is made available via the ade4 package in typical fashion. Results are stored in the reducedDims and are available for all the expected functions.

Usage

calculateDPCoA(x, y, ...)

## S4 method for signature 'ANY,ANY'
calculateDPCoA(
  x,
  y,
  ncomponents = 2,
  ntop = NULL,
  subset_row = NULL,
  scale = FALSE,
  transposed = FALSE,
  ...
)

## S4 method for signature 'TreeSummarizedExperiment,missing'
calculateDPCoA(
  x,
  ...,
  assay.type = assay_name,
  assay_name = exprs_values,
  exprs_values = "counts",
  tree_name = "phylo"
)

runDPCoA(x, ..., altexp = NULL, name = "DPCoA")

Arguments

x	For calculateDPCoA, a numeric matrix of expression values where rows are features and columns are cells. Alternatively, a TreeSummarizedExperiment containing such a matrix. For runDPCoA a TreeSummarizedExperiment containing the expression values as well as a rowTree to calculate y using cophenetic.phylo.
y	a dist or a symmetric matrix compatible with ade4:dpcoa
...	Currently not used.
ncomponents	Numeric scalar indicating the number of DPCoA dimensions to obtain.
ntop	Numeric scalar specifying the number of features with the highest variances to use for dimensionality reduction. Alternatively NULL, if all features should be used. (default: ntop = NULL)
subset_row	Vector specifying the subset of features to use for dimensionality reduction. This can be a character vector of row names, an integer vector of row indices or a logical vector.
scale	Logical scalar, should the expression values be standardized?
transposed	Logical scalar, is x transposed with cells in rows?
assay.type	a single character value for specifying which assay to use for calculation.
assay_name	a single character value for specifying which assay to use for calculation. (Please use assay.type instead. At some point assay_name will be disabled.)
exprs_values	a single character value for specifying which assay to use for calculation. (Please use assay.type instead.)
tree_name	a single character value for specifying which rowTree will be used in calculation. (By default: tree_name = "phylo")
altexp	String or integer scalar specifying an alternative experiment containing the input data.
name	String specifying the name to be used to store the result in the reducedDims of the output.

Details

In addition to the reduced dimension on the features, the reduced dimension for samples are returned as well as sample_red attribute. eig, feature_weights and sample_weights are returned as attributes as well.

Value

For calculateDPCoA a matrix with samples as rows and CCA dimensions as columns

For runDPCoA a modified x with the results stored in reducedDim as the given name

See Also

plotReducedDim reducedDims

Examples

data(esophagus)
dpcoa <- calculateDPCoA(esophagus)
head(dpcoa)

esophagus <- runDPCoA(esophagus)
reducedDims(esophagus)

library(scater)
plotReducedDim(esophagus, "DPCoA")

microbiome/mia documentation built on April 27, 2024, 4:04 a.m.