gs_get_gates: Gates from gatingset for plotting with ggcyto

In Close-your-eyes/fcexpr: Complement the manual analysis of flow cytometric experiments and organize your fcs files in a consistent way

Gates from gatingset for plotting with ggcyto

Description

Gates from gatingset for plotting with ggcyto

Usage

gs_get_gates(
  gs,
  n_bins = 50^2,
  quantile_lim_filter = c(1e-04, 0.9999),
  min_max_vals = c(0, 300),
  min_max_vals_scatter = c(0, 250000),
  x_statpos_name = 0.9,
  y_statpos_name = 0.9,
  x_statpos_pct = 0.9,
  y_statpos_pct = 0.1,
  statsize_name = 4,
  statsize_pct = 4
)

Arguments

gs	gs a gatingset, e.g. made with fcexpr::wsp_get_gs
n_bins	number of bins in total, will be used equally in x and y direction, bin size is adjusted to ranges in x and y direction
quantile_lim_filter	min,max quantiles of signal intensities to set axis limits to; use quantiles to exclude extreme values
min_max_vals	min,max required signal intensitiy for fluorescence channels of one event in order to condider it for axis limit calculation (to filter extreme values); in logicle transformation
min_max_vals_scatter	min,max required signal intensitiy for scatter channels of one event in order to condider it for axis limit calculation (to filter extreme values); in inverse transformation which is equal to logicle transformation (for scatter channels)
x_statpos_name	x-position for gate name labels
y_statpos_name	y-position for gate name labels
x_statpos_pct	x-position for gate percent labels
y_statpos_pct	y-position for gate percent labels
statsize_name	size of name label
statsize_pct	size of percent label

Value

a data frame to loop over and produce plots with ggcyto

Examples

## Not run: 
gates <- gs_get_gates(gs)

## End(Not run)

Close-your-eyes/fcexpr documentation built on Sept. 29, 2023, 12:27 a.m.