Description Usage Arguments Value Author(s) See Also Examples
flowDensity is an automated clustering algorithm which aims to emulate the current practice of manual sequential gating. It is designed to identify the predefined cell subsets based on the density distribution of the parent cell population by analyzing the peaks of the density curve.
When the density distribution has only one peak:
the first argument that would be used is the percentile, the default value is 95th.
If set to 'NA' then upper will be used when set to 'FALSE/TRUE'.
If both upper and percentiles are set to 'NA' sd.threshold is used when set to 'TRUE'.
If either all these arguments are 'NA', or one of them fails, the algorithm find the best cutoff based on the inflection points and by comparing the position of the peak and the mean of the population.
1 | flowDensity(obj, channels, position,node, ...)
|
obj |
a 'CellPopulation', 'flowFrame' or 'GatingHierarchy' object. |
channels |
a vector of two channel names or their corresponding indices. |
position |
a vector of two logical values specifying the position of the cell subset of interest on the 2D plot. |
node |
A character defining the parent population when extracting data from GatingHierarchy. |
... |
This can be used to pass one of the following arguments:
|
A CellPopulation object
Mehrnoush Malek <mmalekes@bccrc.ca> Jafar Taghiyar <jtaghiyar@bccrc.ca>
deGate
getflowFrame
notSubFrame
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