cyto_spillover_compute
uses the method described by Bagwell & Adams
1993 to automatically calculate the fluorescent spillover matrix using single
stain compensation controls.
cyto_spillover_compute( x, parent = NULL, axes_trans = NULL, channel_match = NULL, spillover = NULL, axes_limits = "machine", ... )
x | object of class |
---|---|
parent | name of the population to use for the spillover calculation
when a GatingSet object is supplied, set to the last node of the GatingSet
by default (e.g. "Single Cells"). For greater flexibility, users can
specify a parent population for each control, which will be extracted for
the spillover calculation (e.g. Lymphocytes for CD4 APC or Myeloid Cells
for CD11b FITC). The parent populations for each control can also be
specified in a |
axes_trans | object of class
|
channel_match | name of csv file to associate a fluorescent channel with
each of the compensation controls. The |
spillover | name of the output spillover csv file, set to
|
axes_limits | options include |
... | additional arguments passed to |
spillover matrix and write spillover matrix to csv file named in
accordance with spillover
.
cyto_spillover_compute
supports spillover matrix calculation for both
internal or universal unstained reference populations based on channel
selection. cyto_spillover_compute
expects the fluorescent channels of
the samples to be pre-transformed. Attempts will be made to transform the
data internally (using biexponential transformations) if it looks like the
data has not been transformed.
cyto_spillover_compute
begins by the user selecting which fluorescent
channel is associated with each compensation control from a dropdown menu.
The results of these selections are saved to a csv file called
"Compensation-Channels.csv" which can be passed to the channel_match
argument on subsequent runs to bypass the channel selection process. In cases
where multiple controls are supplied for the same channel, the control with
the greatest signal in the designated channel (MedFI) will be used for the
calculation.
Following channel selection, cyto_spillover_compute
runs through each
compensation control and plots the density distribution in the associated
channel. If a universal "Unstained" compensation control is supplied, the
unstained compensation control will be overlaid onto the plot as a reference
for gating. Users can then gate the positive signal for spillover calculation
using an interval gate. If no universal unstained compensation control is
supplied, users are expected to gate the negative and then the positive
signal for each compensation control.
The percentage spillover is calculated based on the median fluorescent intensities (MedFI) of the positive populations relative to that of the reference negative population(s). The calculated spillover matrix is returned and written to a named csv file for future use.
C. B. Bagwell \& E. G. Adams (1993). Fluorescence spectral overlap compensation for any number of flow cytometry parameters. in: Annals of the New York Academy of Sciences, 677:167-184.
Dillon Hammill, Dillon.Hammill@anu.edu.au
if (FALSE) { library(CytoExploreRData) # Bypass directory check for external files options("CytoExploreR_wd_check" = FALSE) # Load in compensation controls fs <- Compensation gs <- GatingSet(Compensation) # Gate using cyto_gate_draw gt <- Compensation_gatingTemplate cyto_gatingTemplate_apply(gs, gt) # Channel match fille cmfile <- system.file("extdata", "Compensation-Channels.csv", package = "CytoExploreRData" ) # Compute fluorescent spillover matrix spill <- cyto_spillover_compute(cyto_extract(gs, "Single Cells"), channel_match = cmfile, spillover = "Example-spillover.csv" ) # Compensate samples gs <- cyto_compensate(gs, spill) # Return CytoExploreR_wd_check to default options("CytoExploreR_wd_check" = TRUE) }