do.logicle: Using logicle to transform data

In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis

Using logicle to transform data

Description

The function transform data using logicle transformation. It makes use of flowCore's implementation of logicle transformation, and can either automatically infer the transformation function based on your data, or calculate it based on what you want by looking at the default or overriden linearisation.width, max.scale.val, full.transform.width, additional.negative.range. Description of some of the parameter is adapted from flowCore's vignette. For more information on what logicle transformation does, please read the manuscript in the references section.

Usage

do.logicle(dat, use.cols, linearisation.width, max.scale.val, 
full.transform.width, additional.negative.range)

do.logicle(dat, use.cols, auto.infer.function = TRUE,
linearisation.width = 1.2, max.scale.val = 262144, full.transform.width = 4.5,
additional.negative.range = 0)

Arguments

dat	NO DEFAULT. data.table. Input data
use.cols	NO DEFAULT. Vector of column names to transform
auto.infer.function	Default = TRUE. Automatically infer the logical transformation function based on your data. If this is set to FALSE, default or overriden linearisation.width, max.scale.val, full.transform.width, additional.negative.range will be used instead to calculate the logical transformation function.
linearisation.width	Default = 1.2. Linearisation width in asymptotic decades. This must be > 0 and determines the slope of transformation at zero. We found 1.2 works well for flow data, and 0.5 works well for cytof data. It can be estimated using equation: (m-log10(max.scale.val/|r|))/2 where r is the most negative value to included in the display. See max.scale.val below.
max.scale.val	Default = 262144. Maximum scale data value. It can be 10,000 for common 4 decade data or 262144 (the default value) for 18 bit data range. This must be greater than 0
full.transform.width	Default = 4.5. The full width of the transformed values in asymptotic decades This must be greater than 0
additional.negative.range	Default = 0. Additional negative range to be included in the transformed value in asymptotic decades. Value greater than 0 will bring the prescribed additional range into the transformed values

References

Parks, David R., Mario Roederer, and Wayne A. Moore. "A new “Logicle” display method avoids deceptive effects of logarithmic scaling for low signals and compensated data." Cytometry Part A: The Journal of the International Society for Analytical Cytology 69.6 (2006): 541-551.

Examples

library(Spectre)
dat = Spectre::demo.clustered[, 2:9]
use.cols = names(dat)
do.logicle(dat, use.cols = use.cols)

ImmuneDynamics/Spectre documentation built on Oct. 12, 2024, 7:55 p.m.