Edit spillover matrices in real-time using a shiny interface.
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object of class
name of the pre-gated population to be plotted (e.g. "Single Cells").
name of .csv file containing the names of the samples in
a column called "name" and their matching channel in a column called
name of spillover matrix csv file including .csv file
extension to use as a starting point for editing. If
numeric [0,1] to control the percentage of events to be
plotted. Specifying a value for
object of class
additional arguments passed to
spillover_edit provides an interactive shiny interface for editing
fluorescent spillover matrices.
spillover_edit takes on either a
untransformed single stain compensation controls and a universal unstained
control. It is recommended that samples be pre-gated based on FSC and SSC
parameters to obtain a homogeneous population for calculation of fluorescent
spillover. Users begin by selecting the unstained control and a stained
control from dropdown menus of sample names.
cyto_plot to plot the stained sample and overlay the unstained control
in black. Users should then select the channel associated with the selected
control on the
x axis and go through all other channels on the
axis. The displayed spillover matrix is extracted directly from the
GatingSet unless another
spillover matrix is supplied through the spillover argument. To edit the
spillover matrix simply modify the appropriate cell in the the table. The new
spillover matrix will be re-applied to the samples with each edit and
automatically re-plotted so you can track changes in real-time. To aid in
selection of an appropriate spillover value, the median fluorescent intensity
of the unstained control is indicated by a red line and median fluorescent
intensity of the stained control is tracked with a purple line. These
features can be turned off by de-selecting the check boxes. Changes to the
spillover matrix are automatically saved to a csv file called
"Spillover-Matrix.csv" in the case where the
spillover is not
specified or to the same name as the specified
save edited spillover matrix to .csv file named "Spillover-matrix.csv" or spillover.
Dillon Hammill, [email protected]
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## Not run: library(CytoRSuiteData) # Load in compensation controls fs <- Compensation gs <- GatingSet(fs) # Gate single cells using gate_draw gt <- Compensation_gatingTemplate gating(gt, gs) # Channel match file cmfile <- system.file("extdata", "Compensation-Channels.csv", package = "CytoRSuiteData" ) # Edit spillover matrix spillover_edit(gs, parent = "Single Cells", channel_match = cmfile ) ## End(Not run)
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