PlotPeacoQC: Visualise deleted cells of PeacoQC
In PeacoQC: Peak-based selection of high quality cytometry data

Description Usage Arguments Value Examples

View source: R/PeacoQC.R

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.

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PlotPeacoQC(ff, channels, output_directory=".", display_cells=5000,
            manual_cells=NULL, title_FR=NULL, display_peaks=TRUE,
            prefix="PeacoQC_", time_unit=100, ...)

`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 5000.
`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.
`...`	Arguments to be given to `PeacoQC` if `display_peaks` is set to TRUE.

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

## 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)