celda: CEllular Latent Dirichlet Allocation

reorderCelda

R Documentation

Reorder cells populations and/or features modules using hierarchical clustering

Description

Apply hierarchical clustering to reorder the cell populations and/or feature modules and group similar ones together based on the cosine distance of the factorized matrix from factorizeMatrix.

Usage

reorderCelda(
  x,
  celdaMod,
  useAssay = "counts",
  altExpName = "featureSubset",
  method = "complete"
)

## S4 method for signature 'SingleCellExperiment,ANY'
reorderCelda(
  x,
  useAssay = "counts",
  altExpName = "featureSubset",
  method = "complete"
)

## S4 method for signature 'matrix,celda_CG'
reorderCelda(x, celdaMod, method = "complete")

## S4 method for signature 'matrix,celda_C'
reorderCelda(x, celdaMod, method = "complete")

## S4 method for signature 'matrix,celda_G'
reorderCelda(x, celdaMod, method = "complete")

Arguments

`x`	Can be one of A SingleCellExperiment object returned by celda_C, celda_G or celda_CG, with the matrix located in the `useAssay` assay slot in `altExp(x, altExpName)`. Rows represent features and columns represent cells. Integer count matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate `celdaMod`.
`celdaMod`	Celda model object. Only works if `x` is an integer counts matrix. Ignored if `x` is a SingleCellExperiment object.
`useAssay`	A string specifying which assay slot to use if `x` is a SingleCellExperiment object. Default "counts".
`altExpName`	The name for the altExp slot. Default "featureSubset".
`method`	Passed to hclust. The agglomeration method to be used to be used. Default "complete".

Value

A SingleCellExperiment object (or Celda model object) with updated cell cluster and/or feature module labels.

Examples

data(sceCeldaCG)
reordersce <- reorderCelda(sceCeldaCG)
data(celdaCGSim, celdaCGMod)
reorderCeldaCG <- reorderCelda(celdaCGSim$counts, celdaCGMod)
data(celdaCSim, celdaCMod)
reorderCeldaC <- reorderCelda(celdaCSim$counts, celdaCMod)
data(celdaGSim, celdaGMod)
reorderCeldaG <- reorderCelda(celdaGSim$counts, celdaGMod)

campbio/celda documentation built on April 5, 2024, 11:47 a.m.