Reorder cells populations and/or features modules using hierarchical clustering

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.

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

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

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

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

# S4 method for 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)
#> Cluster labels are converted to factors.
#> Module labels are converted to factors.
data(celdaCGSim, celdaCGMod)
reorderCeldaCG <- reorderCelda(celdaCGSim$counts, celdaCGMod)
data(celdaCSim, celdaCMod)
reorderCeldaC <- reorderCelda(celdaCSim$counts, celdaCMod)
data(celdaGSim, celdaGMod)
reorderCeldaG <- reorderCelda(celdaGSim$counts, celdaGMod)