getCellGroups: getCellGroups

In waldronlab/SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets

getCellGroups

Description

Shows the cells/barcodes in two different plots (scatter and density) divinding the space in four quadrant indicated by the two thresholds given as input parameters. The x/y-axis represent respectively the two ADTs given as input. It returns a list of one element for each quadrant, each with barcodes and percentage (see Value section for details).

Usage

getCellGroups(mat, adt1 = "CD19", adt2 = "CD3", th1 = 0.2, th2 = 0)

Arguments

mat	matrix of counts or clr transformed counts for ADT data in CITEseq
adt1	character indicating the name of the marker to plot on the x-axis (default is CD19).
adt2	character indicating the name of the marker to plot on the y-axis (default is CD3).
th1	numeric indicating the threshold for the marker on the x-axis (default is 0.2).
th2	numeric indicating the threshold for the marker on the y-axis (default is 0).

Details

helps to do manual gating for cell type indentification with CITEseq or similar data, providing cell markers. Once identified two interesting markers for a cell type, the user has to play with the thresholds to identify the cell populations specified by an uptake (+) o downtake (-) of the couple of markers (ADTs) previously selected.

Value

a list of four different element, each one indicating the quarter where the thresholds divide the plotting space, in eucledian order I, II, III, IV quadrant, indicating respectively +/+, +/-, -/+, -/- combinations for the couples of selected ADTs. Each element of the list contains two objects, one with the list of detected barcodes and one indicating the percentage of barcodes falling into that quadrant. .

waldronlab/SingleCellMultiModal documentation built on May 1, 2024, 5:29 a.m.