Data Scales

Scales (or “transformations”) are commonly used to improve visualization of cytometry data. Scales are only used for gating and for displaying dot plots and histograms; statistics are calculated on raw, compensated data.

Minimum and maximum values

All scales have minimum and maximum values. Data points outside of this range are shown as a pile-up on the axes. Gates that include the minimum or maximum scale value will include all datapoints below or above the minimum or maximum, respectively.

Scale Types

Linear

Linear scales do not affect the data, except that data is clamped within the minimum and maximum values as described above.

Log

Log scales apply the common logarithm function (log10). Because \(\log(x)\) approaches negative infinity as \(x\) approaches zero, all log scales have a minimum value of 1.0.

ArcSinh (inverse hyperbolic sine)

A limitation of the log scale is the inability to show values at or below zero. The arcsinh function is log-like, but is able to show zero and negative values.

The cofactor parameter adjusts “compression” around zero by dividing the input by this value.

The explicit formula is \(ArcSinh(\frac{x}{c})\). This scale type is generally interchangeable with “biexponential” or “logicle” scales.

Biexponential Scales

Biexponential scales are not yet supported. ArcSinh is a close approximation to biexponential scales.

Changing scales after gating

If you change a scale type or arcsinh cofactor after gating, CellEngine will re-fit the gate coordinates to the new scale. However, because log and arcsinh are non-linear functions, gate edges that were straight with one scale may be curved with another scale. CellEngine does not use curved gate edges; thus, the adjusted gate is only approximately positioned. Depending on the magnitude of the scale change, your gates may require adjustments after changing a scale.

Importing scales from other experiments

You can import scales from another experiment from the gating page.