Apply fluorescence compensation to samples

cyto_compensate will apply a saved spillover matrix csv file to all samples. The csv file must contain the fluorescent channels as both the colnames (i.e. first row) and rownames (i.e. first column). If no spillover csv file is supplied, the spillover matrix will be extracted directly from the first element of x. To select a different sample for spillover matrix extraction supply the index or name of the sample to the select argument. Compensation applied to samples can be easily removed by setting the remove argument to TRUE.

cyto_compensate(x, ...)

# S3 method for GatingSet
cyto_compensate(x, spillover = NULL, select = 1, remove = FALSE, ...)

# S3 method for flowSet
cyto_compensate(x, spillover = NULL, select = 1, remove = FALSE, ...)

# S3 method for flowFrame
cyto_compensate(x, spillover = NULL, select = 1, remove = FALSE, ...)

Arguments

x	object of class flowFrame, flowSet or GatingSet.
...	not in use.
spillover	name of the spillover matrix csv file (e.g. "Spillover-Matrix.csv") saved in the current working directory or spillover matrix object of class matrix or data.frame with channel names assigned to each column. If supplied, spillover will be applied to all samples.
select	index or name of the sample from which the spillover matrix should be extracted when no spillover matrix file is supplied to spillover. To compensate each sample individually using their stored spillover matrix file, set select to NULL.
remove	logical indicating whether applied compensation should be removed from the supplied samples, set to FALSE by default.

Value

a compensated flowFrame, flowSet or GatingSet object.

Author

Dillon Hammill, Dillon.Hammill@anu.edu.au

Examples

# Load in CytoExploreRData to access data
library(CytoExploreRData)

# Apply stored spillover matrix to flowSet
cyto_compensate(Activation)
#> A flowSet with 33 experiments.
#> 
#> column names(18): FSC-A FSC-H ... APC-Cy7-A Time
#> 

# Save spillover matrix in correct format
spill <- cyto_spillover_extract(Activation)[[1]]
rownames(spill) <- colnames(spill)
write.csv(
  spill,
  "Spillover-Matrix.csv"
)

# Apply saved spillover matrix csv file to flowSet
cyto_compensate(Activation, "Spillover-Matrix.csv")
#> A flowSet with 33 experiments.
#> 
#> column names(18): FSC-A FSC-H ... APC-Cy7-A Time
#> 

# Apply stored spillover matrix to GatingSet
gs <- GatingSet(Activation)
cyto_compensate(gs)
#> A GatingSet with 33 samples

# Remove applied compensation
cyto_compensate(gs, remove = TRUE)
#> A GatingSet with 33 samples

# Apply saved spillover matrix csv file to GatingSet
cyto_compensate(gs, "Spillover-Matrix.csv")
#> A GatingSet with 33 samples