Annotate Specific Spots within a SpatialExperiment Object
annotate_spots.Rd
This function allows for the annotation of specified spots within a SpatialExperiment
object.
Users can define a list of spots to be annotated and assign positive or negative values to these spots.
This is particularly useful for distinguishing or marking spots based on certain criteria or experimental results.
Arguments
- spe
A
SpatialExperiment
object representing the spatially resolved data. This is the target object where the annotations will be applied.- spots
A character vector or list specifying the spots within the
SpatialExperiment
object to annotate. These spots should correspond to the column names of theSpatialExperiment
object that represent specific spatial locations or features.- value_pos
The value to assign to the spots specified in the
spots
parameter. This value denotes a positive annotation, indicating that the spots meet a certain condition or criterion.- value_neg
The value to assign to spots not specified in the
spots
parameter. This value denotes a negative annotation, indicating that the spots do not meet the specified condition or criterion.- name
A character string specifying the name of the annotation. This name will be used to label the column in the
SpatialExperiment
object that contains the annotation values.
Value
Returns a SpatialExperiment
object that includes the new annotations.
The function adds a column to the colData
of the SpatialExperiment
object, where the column name is specified by the name
parameter.
Spots specified in the spots
parameter are annotated with the value_pos
value, while all other spots are annotated with the value_neg
value.