reorderCelda {celda} | 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)

[Package celda version 1.8.1 Index]