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Plot Timer Gating Confirmation

Source: R/TockyDataPreprocessing.R
plot_timer_gating.Rd

Generates a plot of the negative control data with gating thresholds overlaid, allowing for visual confirmation of gating parameters used during the timer transformation process.

Usage 

plot_timer_gating(prep, x)

Arguments

prep

A list containing file paths and variables, typically the output from prep_tocky. It must include:

  • neg: Character string specifying the negative control file name.

  • path: Character string specifying the directory path to data files.

x

A TockyPrepData object resulting from timer_transform, containing processed data and normalization parameters, including gating thresholds.

Value

This function generates a plot; it does not return a value.

Details

This function reads the negative control data specified in prep, applies logarithmic transformation to the Timer Red and Timer Blue fluorescence channels, and plots Red_log versus Blue_log values. The gating thresholds extracted from the TockyPrepData object x are overlaid on the plot as vertical and horizontal lines. This allows users to visually confirm the gating thresholds applied during the data normalization process.

Examples 

if (FALSE) { # \dontrun{
# Assuming 'prep_data' is the output from 'prep_tocky' and 'tocky_data' is the TockyPrepData object
plot_timer_gating(prep = prep_data, x = tocky_data)
} # }