Visualize MFI of raw .fcs files to evaluate single color controls.
Source:R/Luciernaga_Brightness.R
Luciernaga_Brightness.RdVisualize MFI of raw .fcs files to evaluate single color controls.
Usage
Luciernaga_Brightness(
fluorophore.name,
data,
fluorophore.column,
cluster.column,
downsample = TRUE,
subsample = NULL,
detector = NULL,
reference = NULL,
clearance = 0.02,
Scaled = TRUE,
maxtik = 1e+06,
legend = "right"
)Arguments
- fluorophore.name
The name of the fluorophore to filter from data
- data
The data.frame derrived by Luciernaga_FolderBrightness, consisting of fluorophore and cluster metadata, and the raw detector values
- fluorophore.column
The name of the column containing the fluorophore information
- cluster.column
The name of the column containing the cluster information
- downsample
Default is TRUE, to avoid having large populations take over the entire y-axis.
- subsample
When downsample is true, number of cells from each cluster to keep. The default NULL will select the number of cells found in the smallest cluster
- reference
A .csv path or data.frame containing Fluorophore and Detector information from which to retrieve the x-axis detector, use same naming as with the passed fluorophore argument in x
- clearance
A buffer area multiplier to xmin and xmax when scaled equals false
- Scaled
Default is set to TRUE, returning log_10 transformed data, FALSE will return raw MFI.
- maxtik
Default is 1e6
- legend
Default is "right"
- Detector
Default NULL, when reference is NULL sets the detector to plot on the x-axis