Calculation of Double Principal Correspondance analysis

Source: R/runDPCoA.R

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.

getDPCoA(x, y, ...)

# S4 method for class 'ANY,ANY'
getDPCoA(
  x,
  y,
  ncomponents = 2,
  ntop = NULL,
  subset.row = subset_row,
  subset_row = NULL,
  scale = FALSE,
  transposed = FALSE,
  ...
)

# S4 method for class 'TreeSummarizedExperiment,missing'
getDPCoA(
  x,
  ...,
  assay.type = assay_name,
  assay_name = exprs_values,
  exprs_values = "counts",
  tree.name = tree_name,
  tree_name = "phylo"
)

calculateDPCoA(x, ...)

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

runDPCoA(x, ...)

Arguments

x

TreeSummarizedExperiment.

y

a dist or a symmetric matrix compatible with ade4:dpcoa

...

Currently not used.

ncomponents

Numeric scalar. Indicates the number of DPCoA dimensions to obtain. (Default: 2)

ntop

Numeric scalar. Specifies the number of features with the highest variances to use for dimensionality reduction. Alternatively NULL, if all features should be used. (Default: NULL)

subset.row

Character Vector. Specifies 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. (Default: NULL)

subset_row

Deprecated. Use subset.row instead.

scale

Logical scalar. Should the expression values be standardized? (Default: FALSE)

transposed

Logical scalar. Specifies if x is transposed with cells in rows. (Default: FALSE)

assay.type

Character scalar. Specifies which assay to use for calculation. (Default: "counts")

assay_name

Deprecated. Use assay.type instead.

exprs_values

Deprecated. Use assay.type instead.

tree.name

Character scalar. Specifies the name of the tree to be included in the phyloseq object that is created, (Default: "phylo")

tree_name

Deprecated. Use tree.name instead.

altexp

Character scalar or integer scalar. Specifies an alternative experiment containing the input data. (Default: NULL)

name

Character scalar. A name for the column of the colData where results will be stored. (Default: "DPCoA")

Value

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

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

Details

For addDPCoA a TreeSummarizedExperiment containing the expression values as well as a rowTree to calculate y using cophenetic.phylo.

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.

Examples

data(esophagus)
dpcoa <- getDPCoA(esophagus)
head(dpcoa)
#>          [,1]         [,2]
#> B -0.05368615  0.046589779
#> C -0.04324591 -0.039790060
#> D  0.10011870  0.003144932

esophagus <- addDPCoA(esophagus)
reducedDims(esophagus)
#> List of length 1
#> names(1): DPCoA

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