normQA | R Documentation |
Create QA plots for a flow cytometry normalization process.
normQA(data, morph = c("^fsc", "^ssc"),
channels, odat = NULL, ask = names(dev.cur()) != "pdf",
grouping = NULL, tag.outliers = FALSE, peaksOnly = TRUE)
data |
a normalized |
morph |
A character vector of channel names to use for the backgating into the morphological channels. |
channels |
The channels for which to create plots. Defaults to all normalized channels. |
odat |
The original data set, always needed if there are no warping functions available. |
ask |
Ask before creating a new plot. |
grouping |
A grouping variable in |
tag.outliers |
Logical. Add sample name to outliers in the plots. |
peaksOnly |
Logical. Only use data when a peak was detected in a
particular sample. If set to |
This function assumes that the necessary information has been added as
attributes to data
during the normalization procedure. Depending
on the available information, a set of QA plots is generated.
Available plots are:
Amount of peak adjustment
Warping functions
Landmark classification confidence
Backgating of peak events in morphological channels
This function is called for its side effect of generating plots.
Florian Hahne
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