splitscale-class {flowCore} | R Documentation |
The split scale transformation class defines a transformation that has a logarithmic scale at high values and a linear scale at low values. The transition points are chosen so that the slope of the transformation is continuous at the transition points.
The split scale transformation is defined by the function
f(parameter,r,maxValue,transitionChannel)= a*parameter+ b ~~~~parameter<=t
log_{10}(c*parameter)*\frac{r}{d} ~~~~parameter > t
where,
b=\frac{transitionChannel}{2}
d=\frac{2*log_{10}(e)*r}{transitionChannel} + log_{10}(maxValue)
t=10^{log_{10}t}
a= \frac{transitionChannel}{2*t}
log_{10}ct=\frac{(a*t+b)*d}{r}
c=10^{log_{10}ct}
Objects can be created by calls to the constructor
splitscale(parameters,r,maxValue,transitionChannel,transformationId)
.Data
:Object of class "function"
~~
r
:Object of class "numeric"
-a positive value indicating the range of the logarithmic
part of the display
maxValue
:Object of class "numeric"
-a positive value indicating the maximum value the transformation
is applied to
transitionChannel
:Object of class "numeric"
-non negative value that indicates where to
split the linear vs. logarithmic transformation
parameters
:Object of class "transformation"
- flow parameter to be transformed
transformationId
:Object of class "character"
-unique ID to reference the transformation
Class "singleParameterTransform"
, directly.
Class "transform"
, by class "singleParameterTransform", distance 2.
Class "transformation"
, by class "singleParameterTransform", distance 3.
Class "characterOrTransformation"
, by class "singleParameterTransform", distance 4.
No methods defined with class "splitscale" in the signature.
The transformation object can be evaluated using the eval method by passing the data frame as an argument.The transformed parameters are returned as a matrix with a single column. (See example below)
Gopalakrishnan N, F.Hahne
Gating-ML Candidate Recommendation for Gating Description in Flow Cytometry
invsplitscale
dat <- read.FCS(system.file("extdata","0877408774.B08",package="flowCore")) sp1<-splitscale("FSC-H",r=768,maxValue=10000,transitionChannel=256) transOut<-eval(sp1)(exprs(dat))