spillover_edit: Edit Spillover Matrix

In DillonHammill/cytoSuite: Compensation, Gating & Visualisation Toolkit for Analysis of Flow Cytometry Data

Description

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

Usage

spillover_edit(x, ...)

Arguments

x	object of class flowSet or flowSet.
...	additional method-specific arguments.

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. spillover_edit has methods for both flowSet and flowSet objects refer to their respective help pages for more information.

Author(s)

Dillon Hammill, [e-mail]

See Also

spillover_edit,flowSet-method

spillover_edit,GatingSet-method

cyto_plot,flowFrame-method

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