Interactively determine gates to define negative (and positive) regions for each marker expression

This function allows interactive setting of thresholds on plots to define negative and positive gates for markers. Users can choose to plot data as 2D scatter plots or as density plots, and may utilize pseudocolor to enhance visualization.

Usage

DefineNegatives(
  x,
  select = TRUE,
  max_cells_displayed = 30000,
  y_axis_var = NULL,
  pseudocolour = TRUE
)

Arguments

x

A FlowObject containing the data.

select

Logical, whether to interactively select markers to be processed. If FALSE, all logged expression variables will be used. Default is TRUE.

max_cells_displayed

Maximum number of cells displayed in plots for determining a negative threshold.

y_axis_var

The variable to use for the y-axis in the interactive plot, or 'Density' to use a density plot. If NULL (default), the user will be prompted to select a variable from x@Data.

pseudocolour

Logical, whether to use pseudocolor based on density in scatter plots. Default is TRUE. The option FALSE will use monochrome.

Value

A modified FlowObject containing updated threshold values for autofluorescence in the selected variables in the slot QCdata. You can repeat DefineNegatives to renew or adjust some or all of the negative thresholds for variables.

See also

Other Data Transformation: LogData(), NormAF(), PlotDefineNegatives(), PlotNormAF()

Examples

if (FALSE) { # \dontrun{
x <- DefineNegatives(x)
} # }