PlotPeacoQC: Visualise deleted cells of PeacoQC

In saeyslab/PeacoQC: Peak-based selection of high quality cytometry data

Visualise deleted cells of PeacoQC

Description

PlotPeacoQC will generate a png file with on overview of the flow rate and the different selected channels. These will be annotated based on the measurements that were removed by PeacoQC. It is also possible to only display the quantiles and median or only the measurements without any annotation.

Usage

PlotPeacoQC(ff, channels, output_directory=".", display_cells=2000,
            manual_cells=NULL, title_FR=NULL, display_peaks=TRUE,
            prefix="PeacoQC_", time_unit=100, time_channel_parameter="Time",
             ...)

Arguments

ff	A flowframe
channels	Indices of names of the channels in the flowframe that have to be displayed
output_directory	Directory where the plots should be generated. Set to NULL if no plots need to be generated. The default is the working directory.
display_cells	The number of measurements that should be displayed. (The number of dots that are displayed for every channel) The default is 2000.
manual_cells	Give a vector (TRUE/FALSE) with annotations for each cell to compare the automated QC with. The default is NULL.
title_FR	The title that has to be displayed above the flow rate figure. Default is NULL.
display_peaks	If the result of PeacoQC is given, all the quality control results will be visualised. If set to TRUE: PeacoQC will be run and only the peaks will be displayed without any quality control. If set to FALSE, no peaks will be displayed and only the events will be displayed. Default is TRUE.
prefix	The prefix that will be given to the generated png file. Default is "PeacoQC_".
time_unit	The number of time units grouped together for visualising event rate. The default is set to 100, resulting in events per second for most flow datasets. Suggested to adapt for mass cytometry data.
time_channel_parameter	Name of the time channel in ff if present. Default is "Time".
...	Arguments to be given to PeacoQC if display_peaks is set to TRUE.

Value

This function returns nothing but generates a png file in the output_directory

Examples

## Plotting the results of PeacoQC

# Read in transformed and compensated data
fileName <- system.file("extdata", "111_Comp_Trans.fcs", package="PeacoQC")
ff <- flowCore::read.FCS(fileName)

# Define channels on which the quality control should be done and the
# plots should be made
channels <- c(1, 3, 5:14, 18, 21)

# Run PeacoQC
PeacoQC_res <- PeacoQC(ff,
    channels,
    determine_good_cells="all",
    plot=FALSE,
    save_fcs=TRUE)

# Run PlotPeacoQC
PlotPeacoQC(ff, channels, display_peaks=PeacoQC_res)

## Plot only the peaks (No quality control)
PlotPeacoQC(ff, channels, display_peaks=TRUE)

## Plot only the dots of the file
PlotPeacoQC(ff, channels, display_peaks=FALSE)

saeyslab/PeacoQC documentation built on Aug. 24, 2023, 8:11 a.m.