R/Response_surface.R

In Michorlab/ACESO: A Cancer Evolution Simulation Optimizer

#' @import ggplot2
NULL

#' responseMap
#' 
#' @param model a two-column array containing the values of input 1 and input 2 in each data point, or a symbolic formula (e.g. act ~ conc1+conc2) specifying which variables are to be visualized
#' @param data  if model is an array, a vector of values in response to inputs 1 and 2; if model is a formula, a data frame containing the columns specified in formula
#' @param irreg reflects whether or not data points lie in a regularly-spaced grid in the space of data points to be plotted
#' @param interpolate determines whether the plot will produce a smoothed response surface using Gaussian interpolation, or if the space will be visualized as a set of discrete measurements using nearest neighbor segmentation
#' @param margins determines whether input pairs in which one of the two inputs is zero will be plotted; applies only to logarithmically scaled plots
#' @param logscale determines whether the input variables will be plotted on a logarithmic scale, or a standard linear scale. Because this function is intended primarily for visualizing combined action dose-response, a logarithmic dose-pair space is the default.
#' @param zlims an optional parameter specifying lower and upper bounds on the response variable. If present, all effect values outside the given range will be clipped to the minimum and maximum values
#' @param raster by default, interpolated response surfaces will be rendered using the ggplot2 function geom_raster, a faster and optimized raster image version of geom_tile. In certain settings, however, geom_raster can produce unusual appearance. Setting this parameter to FALSE will force the plot to be rendered using geom_tile.
#' @return A ggplot2 plot object, depicting the response variable (represented by the plot\'s \'fill\' variable) as a function of two inputs (the x- and y-dimensions).
#' @author Nathaniel R. Twarog
#' @references Twarog, N.R., Stewart, E., Vowell Hamill, C., and Shelat, A. BRAID: A Unifying Paradigm for the Analysis of Combined Drug Action. Scientific Reports In Press (2016).
#' @seealso braidReports::responseMap
#' @export
#' @examples 
#' \dontrun{
#' data(Dactolisib_Trametinib_combination)
#' growth_data<-net_growth_rate(Dactolisib_Trametinib_combination)
#' rmap <- responseMap(Net_growth~CONC+CONC2,GD,logscale=T)
#'
#' ResponseSurface.plot(rmap,xl=expression(paste("[Dactolisib] (",mu,"M)", sep="")),
#'                     yl=expression(paste("[Trametinib] (",mu,"M)", sep="")),
#'                     zl="Net growth rate of \n sensitive cells",
#'                    palette=c("hotpink1","yellow","darkturquoise"))
#' }
responseMap<-function(model,data,irreg=FALSE,interpolate=TRUE,margins=TRUE,
                      logscale=TRUE,zlims=NULL,raster=TRUE){
  return(braidReports::responseMap(model=model,data=data,irreg=irreg,interpolate=interpolate,margins=margins,
                                   logscale=logscale,zlims=zlims,raster=raster))
}

#' ResponseSurface.plot
#'
#' 
#'
#' @param rmap a ggplot2 plot object depicting a response map, produced by the function responseMap.
#' @param palette a character vector or two or more colors defining the colorscale to be applied to the fill variable in the plot.
#' @param cscale a value around which the colorscale applied to the fill variable will be centered. If NULL (the default), the colorscale will range from the minimum fill variable to the maximum.
#' @param xl The character string or expression used to label the x-axis
#' @param yl The character string or expression used to label the y-axis
#' @param zl The character string or expression used to label the colorscale representing the response variable. "Effect" by default.
#' @param title title for the plot
#' @return A ggplot2 plot object, with the appropriate scales and labels added.
#' @seealso braidReports::responseMap
#' @export
#' @examples 
#' \dontrun{
#' data(Dactolisib_Trametinib_combination)
#' growth_data<-net_growth_rate(Dactolisib_Trametinib_combination)
#' rmap <- braidReports::responseMap(Net_growth~CONC+CONC2,GD,logscale=T)
#'
#' ResponseSurface.plot(rmap,xl=expression(paste("[Dactolisib] (",mu,"M)", sep="")),
#'                     yl=expression(paste("[Trametinib] (",mu,"M)", sep="")),
#'                     zl="Net growth rate of \n sensitive cells",
#'                    palette=c("hotpink1","yellow","darkturquoise"))
#' }

ResponseSurface.plot <- function(rmap,palette=NULL,cscale=NULL,xl=expression(CONC),yl=expression(CONC2),zl="Effect",title="") {
  fp <- rmap+labs(x=xl,y=yl)+ stat_contour(aes(z = rmap$data$z),colour="black", alpha=.2) +ggtitle(paste(title))
  if (is.null(palette)) { palette=c("magenta","yellow","darkturquoise") }
  if (!is.null(cscale)) {
    if (length(cscale)>1) { cscale <- cscale[1] }
    totmin <- min(rmap$data$z)
    totmax <- max(rmap$data$z)
    for (i in 1:length(rmap$layers)) {
      if (!is.null(rmap$layers[[i]]$data$z)) {
        totmin <- min(totmin,min(rmap$layers[[i]]$data$z))
        totmax <- max(totmax,max(rmap$layers[[i]]$data$z))
      }
    }
    dev <- max(totmax-cscale,cscale-totmin)+0.01
    clims <- c(cscale-dev,cscale+dev)
    fp <- fp + scale_fill_gradientn(zl,limits=clims,colours=palette)+theme_minimal()+ theme(text = element_text(size=14))
  } else { fp <- fp + scale_fill_gradientn(zl,colours=palette)+theme_minimal()+ theme(text = element_text(size=14)) }

  return(fp)
}

#' DifferenceSurface.plot
#'
#' 
#'
#' @param rmap a ggplot2 plot object depicting a response map, produced by the function responseMap.
#' @param zcenter the value that forms the centerpoint (white) in the bidirectional color scale. If NULL (the default), the default setting for scale_fill_gradient2 is used.
#' @param xl The character string or expression used to label the x-axis
#' @param yl The character string or expression used to label the y-axis
#' @param zl The character string or expression used to label the colorscale representing the response variable. "Effect" by default.
#' @param low character corresponding to the color selected for the lowest values in the response map.
#' @param mid color for the mid point.
#' @param high character corresponding to the color selected for the highest values in the response map.
#' @param title title for the plot
#' @return A ggplot2 plot object, with the appropriate scales and labels added.
#' @seealso braidReports::responseMap
#' @export
#' @examples 
#' \dontrun{
#' data(Dactolisib_Trametinib_combination)
#' growth_data<-net_growth_rate(Dactolisib_Trametinib_combination)
#' GD=growth_data[,c('Cell.line','CONC','CONC2','Net_growth','Type','Birth_rate','Death_rate')]
#' GD=unique(GD)
#' rmap <- braidReports::responseMap(Net_growth~CONC+CONC2,GD,logscale=T,interpolate=FALSE)
#' DifferenceSurface.plot(rmap,zcenter=0.01,xl=expression(paste("[Dactolisib] (",mu,"M)", sep="")),
#' yl=expression(paste("[Trametinib] (",mu,"M)", sep="")),
#' zl="Net growth rate of \n sensitive cells",
#' mid="yellow",low="hotpink1",high="darkturquoise")
#'
#' }
DifferenceSurface.plot <- function(rmap,zcenter=NULL,xl=expression(CONC),yl=expression(CONC2),zl="Effect",low="#e9a3c9",mid="#f7f7f7",high="#4dac26",title=""){
  fp <- rmap+labs(x=xl,y=yl)+ggtitle(paste(title))
  if (!is.null(zcenter)) { fp <- fp+scale_fill_gradient2(zl,midpoint=zcenter,mid = mid,low=low,high=high) }
  #if (is.null(palette)) { palette=c("magenta","yellow","darkturquoise") }
  else { fp <- fp+scale_fill_gradient2(zl,mid = mid,low=low,high=high) }
  return(fp)
}