reorderCelda {celda} | R Documentation |
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 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")
x |
Can be one of
|
celdaMod |
Celda model object. Only works if |
useAssay |
A string specifying which assay
slot to use if |
altExpName |
The name for the altExp slot. Default "featureSubset". |
method |
Passed to hclust. The agglomeration method to be used to be used. Default "complete". |
A SingleCellExperiment object (or Celda model object) with updated cell cluster and/or feature module labels.
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)