Obtain molecular signature names

Extracts a character vector of molecular signature names.

getGeneSets(object, ..., class = NULL)

getMetaboliteSets(object, ..., class = NULL)

getProteinSets(object, ..., class = NULL)

getSignatureNames(object, ..., class = NULL, assay_name = activeAssay(object))

Arguments

object

An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.

...

Additional selection helpers from the tidyselect package that match names according to a given pattern.

class

Character vector of signature classes with which to subset the output.

assay_name

Only relevant if the SPATA2 object contains more than one assay: Denotes the assay of interest and thus the molecular modality to use. Defaults to the active assay as set by activateAssay().

Value

Character vector.

Details

These functions retrieve signature names from the provided object.

  • getSignatureNames(): The signature names from the assay specified in assay_name.

  • getGeneSets(): The signature names from the assay with @modality = 'gene' (assay_name = 'gene').

  • getMetaboliteSets(): The signature names from the assay with @modality = 'metabolite' (assay_name = 'metabolite').

  • getProteinSets(): The signature names from the assay with @modality = 'protein' (assay_name = 'protein').

If 'signature' is NULL, it returns all molecules from the respective assay in the object.

See also

vselect(), lselect()

Documentation of slot @signatures in the MolecularAssay-class. To extract character vectors of molecule names getMolecules() or getGenes(), ... To extract character vectors of signature names getSignatureNames(), getGeneSets(), ... To add signatures addSignature() or addGeneSet(), ...

Examples


library(SPATA2)

object <- loadExampleObject("UKF269T", process = TRUE)

# only one assay exists...
getAssayNames(object)

# ... which is the default assay
activeAssay(object)

## extraction
# opt 1
all_signatures <- getSignatureNames(object, assay_name = "gene")

str(all_signatures)

# whether you specify assay_name or not does not make a difference since
# the object only contains one assay
hallmark_signatures <- getSignatureNames(object, class = "HM")

str(hallmark_signatures)

# opt 2
hallmark_signatures <- getGeneSets(object, class = "HM")

str(hallmark_signatures)

# opt 3 - failes cause no 'protein' assay
protein_signatures <- getProteinSets(object, assay_name = "protein")

## usage as character vector for argument input

set.seed(123)
color_by <- sample(all_signatures, size = 9)

plotSurfaceComparison(object, color_by = color_by, outline = T, pt_clrsp = "Reds 3")

coords_df <- getCoordsDf(object)

print(coords_df)

coords_df <- joinWithVariables(object, spata_df = coords_df, variables = hallmark_signatures)

print(coords_df)