spillover_edit-GatingSet-method: Edit Spillover Matrix GatingSet Method

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Edit spillover matrices in real-time using a shiny interface.

Usage

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## S4 method for signature 'GatingSet'
spillover_edit(x, parent = NULL,
  channel_match = NULL, spillover = NULL, display = 1,
  axes_trans = NULL, ...)

Arguments

x

object of class GatingSet.

parent

name of the pre-gated population to be plotted (e.g. "Single Cells").

channel_match

name of .csv file containing the names of the samples in a column called "name" and their matching channel in a column called "channel". spillover_edit will the guide you through the channel selection process and generate a channel match file called "Compensation-Channels.csv" automatically. If you already have a complete channel_match and would like to bypass the channel selection process, simply pass the name of the channel_match to this argument (e.g. "Compensation-Channels.csv").

spillover

name of spillover matrix csv file including .csv file extension to use as a starting point for editing. If spillover is not supplied the spillover matrix will be extracted directly from the GatingSet and the edited matrix saved to "Spillover-Matrix.csv".

display

numeric [0,1] to control the percentage of events to be plotted. Specifying a value for display can substantial improve plotting speed for less powerful machines. Set to all events by default.

axes_trans

object of class transformList or transformerList generated by estimateLogicle which was used to transform the fluorescent channels of the flowSet.

...

additional arguments passed to cyto_plot,flowFrame-method.

Details

spillover_edit provides an interactive shiny interface for editing fluorescent spillover matrices. spillover_edit takes on either a flowSet or GatingSet containing 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. spillover_edit leverages 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 y axis. The displayed spillover matrix is extracted directly from the flowSet or 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 spillover.

Value

save edited spillover matrix to .csv file named "Spillover-matrix.csv" or spillover.

Author(s)

Dillon Hammill, [email protected]

See Also

spillover_edit,flowSet-method

cyto_plot,flowFrame-method

Examples

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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)

DillonHammill/cytoSuite documentation built on March 7, 2019, 10:09 a.m.