kinopt-class {TIMP}R Documentation

Class "kinopt" stores options for fitting and plotting kinetic models

Description

Class "kinopt" stores options for fitting and plotting kinetic models in particular; this is a subclass of class opt

Details

See opt-class for the specification of fitting/plotting options that are not specific to the class type.

Objects from the Class

Objects can be created by calls of the form new("kinopt", ...) or kinopt(...)

Slots

notraces:
Object of class "logical" that defaults to FALSE; if TRUE, do not plot traces
selectedtraces:
Object of class "vector" containing x indices for which plots of traces are desired under a kinetic model
breakdown:
Object of class "list" with the following elements:
FLIM:
Object of class "logical" that defaults to FALSE; if TRUE, the data represent a FLIM experiment and special plots are generated.
FLIMresidimag:
Object of class "logical" that defaults to TRUE; if FALSE and a FLIM image is analyzed, the residuals are not plotted as an image.
noFLIMsummary:
Object of class "logical" that defaults to FALSE; if TRUE and a FLIM image is analyzed, only other plots requested by the user (such as traces or residuals) are generated, and no summary plot in made.
kinspecest
Object of class "logical" that defaults to FALSE; if TRUE, make a plot of the spectra associated with the kinetic components as well as the lifetime estimates.
writeplaincon
Object of class "list"; if length is greater than 0, then the concentration model will be evaluated at the vector of x values supplied as the element "x" of writeplaincon and the result will be written to file for each dataset.
writerawcon
Object of class "logical" that defaults to FALSE; if TRUE, then the representation of the concentration profiles before the application of constraints (to account for the equality of spectra, etc.) is written to file for each dataset.
plotcohcolspec
Object of class "logical" that defaults to TRUE; if FALSE then the spectra associated with the coherent artifact (pulse-follower) are not included in the summary plots
plotpulsefol:
Object of class "logical" defaults to FALSE; if TRUE adding imageplots of pulsefolower amplitudes in summary plot (only with FLIM plots).
ylimcomp
Object of class "vector" that defaults to vector(); Works In the case of plotting the results of FLIM image analysis, ylimspec can be used to determine the range used in the image plot of normalized amplitudes.

Author(s)

Katharine M. Mullen, Ivo H. M. van Stokkum

See Also

examineFit, fitModel, opt-class, specopt-class


[Package TIMP version 1.8 Index]