R/methods-EigensystemPlotParam-class.R

Defines functions figure filenames prefix path negativeValues contrast featureColorMap assayColorMap whichPolarAxes whichEigenfeatures whichEigenassays whichFeatures whichAssays palette plots

Documented in assayColorMap contrast featureColorMap figure filenames negativeValues palette path plots prefix whichAssays whichEigenassays whichEigenfeatures whichFeatures whichPolarAxes

### =========================================================================
### EigensystemPlotParam class methods 
### =========================================================================

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### Getters
###
##' @export
plots <- function(x) slot(x, "plots") 
##' @export
palette <- function(x) slot(x, "palette") 
##' @export
whichAssays <- function(x) slot(x, "whichAssays") 
##' @export
whichFeatures <- function(x) slot(x, "whichFeatures") 
##' @export
whichEigenassays <- function(x) slot(x, "whichEigenassays") 
##' @export
whichEigenfeatures <- function(x) slot(x, "whichEigenfeatures") 
##' @export
whichPolarAxes <- function(x) slot(x, "whichPolarAxes") 
##' @export
assayColorMap <- function(x) slot(x, "assayColorMap") 
##' @export
featureColorMap <- function(x) slot(x, "featureColorMap") 
##' @export
contrast <- function(x) slot(x, "contrast") 
##' @export
negativeValues <- function(x) slot(x, "negativeValues") 
##' @export
path <- function(x) slot(x, "path") 
##' @export
prefix <- function(x) slot(x, "prefix") 
##' @export
filenames <- function(x) slot(x, "filenames") 
##' @export
figure <- function(x) slot(x, "figure") 

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Setters
###

##' Set plots for object of EigensystemPlotParam
##' 
##' Set plots for object of EigensystemPlotParam
##' @title Set plots for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot plots
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"plots<-" <- function(x, value)
{
  slot(x, "plots") <- value
  x
} 

##' Set palette for object of EigensystemPlotParam
##' 
##' Set palette for object of EigensystemPlotParam
##' @title Set palette for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot palette
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"palette<-" <- function(x, value)
{
  slot(x, "palette") <- value
  x
} 

##' Set whichAssays for object of EigensystemPlotParam
##' 
##' Set whichAssays for object of EigensystemPlotParam
##' @title Set whichAssays for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot whichAssays
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"whichAssays<-" <- function(x, value)
{
  slot(x, "whichAssays") <- value
  x
} 

##' Set whichFeatures for object of EigensystemPlotParam
##' 
##' Set whichFeatures for object of EigensystemPlotParam
##' @title Set whichFeatures for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot whichFeatures
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"whichFeatures<-" <- function(x, value)
{
  slot(x, "whichFeatures") <- value
  x
} 

##' Set whichEigenassays for object of EigensystemPlotParam
##' 
##' Set whichEigenassays for object of EigensystemPlotParam
##' @title Set whichEigenassays for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot whichEigenassays
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"whichEigenassays<-" <- function(x, value)
{
  slot(x, "whichEigenassays") <- value
  x
} 

##' Set whichEigenfeatures for object of EigensystemPlotParam
##' 
##' Set whichEigenfeatures for object of EigensystemPlotParam
##' @title Set whichEigenfeatures for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot whichEigenfeatures
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"whichEigenfeatures<-" <- function(x, value)
{
  slot(x, "whichEigenfeatures") <- value
  x
} 

##' Set whichPolarAxes for object of EigensystemPlotParam
##' 
##' Set whichPolarAxes for object of EigensystemPlotParam
##' @title Set whichPolarAxes for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot whichPolarAxes
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"whichPolarAxes<-" <- function(x, value) 
{
  slot(x, "whichPolarAxes") <- value
  x
}

##' Set assayColorMap for object of EigensystemPlotParam
##' 
##' Set assayColorMap for object of EigensystemPlotParam
##' @title Set assayColorMap for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot assayColorMap
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"assayColorMap<-" <- function(x, value)
{
  slot(x, "assayColorMap") <- value
  x
} 

##' Set featureColorMap for object of EigensystemPlotParam
##' 
##' Set featureColorMap for object of EigensystemPlotParam
##' @title Set featureColorMap for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot featureColorMap
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"featureColorMap<-" <- function(x, value)
{
  slot(x, "featureColorMap") <- value
  x
} 

##' Set contrast for object of EigensystemPlotParam
##' 
##' Set contrast for object of EigensystemPlotParam
##' @title Set contrast for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot contrast
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"contrast<-" <- function(x, value)
{
  slot(x, "contrast") <- value
  x
} 

##' Set negativeValues for object of EigensystemPlotParam
##' 
##' Set negativeValues for object of EigensystemPlotParam
##' @title Set negativeValues for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot negativeValues
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"negativeValues<-" <- function(x, value)
{
  slot(x, "negativeValues") <- value
  x
} 

##' Set path for object of EigensystemPlotParam
##' 
##' Set path for object of EigensystemPlotParam
##' @title Set path for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot path
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"path<-" <- function(x, value)
{
  slot(x, "path") <- value
  x
} 

##' Set prefix for object of EigensystemPlotParam
##' 
##' Set prefix for object of EigensystemPlotParam
##' @title Set prefix for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot prefix
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"prefix<-" <- function(x, value)
{
  slot(x, "prefix") <- value
  x
} 

##' Set filenames for object of EigensystemPlotParam
##' 
##' Set filenames for object of EigensystemPlotParam
##' @title Set filenames for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot filenames
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"filenames<-" <- function(x, value)
{
  slot(x, "filenames") <- value
  x
} 

##' Set figure for object of EigensystemPlotParam
##' 
##' Set figure for object of EigensystemPlotParam
##' @title Set figure for object of EigensystemPlotParam
##' @param x object of class Eigensystem
##' @param value new value for slot figure
##' @return object of class Eigensystem
##' @export
##' @seealso EigensystemPlotParam-class
##' @author Anneleen Daemen \email{[email protected]@gene.com}, Matthew Brauer \email{[email protected]@gene.com}
"figure<-" <- function(x, value)
{
  slot(x, "figure") <- value
  x
} 


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### Show
###
setMethod(show, "EigensystemPlotParam",
          function(object)
          {
            cat("class:", class(object), "\n")
            slots <- c("plots","palette","whichAssays",
                       "whichFeatures","whichEigenassays","whichEigenfeatures","whichPolarAxes",
                       "assayColorMap","featureColorMap","contrast",
                       "negativeValues","path","prefix",
                       "filenames","figure")
            for (i in slots) {
              elt <- slot(object, i)
              if(class(elt) == "list")
                cat(i,": ",unlist(elt),"\n")
              else if (!class(elt) %in% "function")
              	cat(i,": ",elt,"\n")
             }
          }
          )

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biosvd documentation built on Nov. 1, 2018, 2:11 a.m.