R/ablandscape_par.R

In acorg/ablandscapes: Making Antibody landscapes Using R

#' Get defaults for antibody landscape plotting
#'
#' This function returns all the options that can be set for plotting of antibody
#' landscapes and the default values for them.
#'
#' @return Returns a list of default plotting options for making antibody landscapes.
#' 
#' @export
#' 
ablandscape.par <- function(
  cex                    = 1,
  cex.basemap            = cex,
  cex.basemap.ags        = cex.basemap,
  cex.basemap.sr         = cex.basemap,
  cex.titer              = cex,
  cex.titer.impulse      = cex,
  col.impulse            = "grey20",
  lwd.impulse            = 0.5,
  lwd.grid               = 1,
  lwd.titer.outline      = 1,
  asp.z                  = 1,
  zaxt                   = "linear",
  col.grid               = "grey80",
  col.surface            = "grey20",
  col.surface.grid       = "grey20",
  shininess.surface      = 30,
  sidegrid.lwd           = 1,
  sidegrid.col           = "grey95",
  sidegrid.at            = NULL,
  opacity.basemap        = 0.4,
  opacity.basemap.ags    = opacity.basemap,
  opacity.basemap.sr     = opacity.basemap,
  opacity.surface        = 0.8,
  opacity.surface.grid   = 0.6
) {
  
  list(
    cex                    = cex,
    cex.basemap            = cex.basemap,
    cex.basemap.ags        = cex.basemap.ags,
    cex.basemap.sr         = cex.basemap.sr,
    cex.titer              = cex.titer,
    cex.titer.impulse      = cex.titer.impulse,
    asp.z                  = asp.z,
    zaxt                   = zaxt,
    col.impulse            = col.impulse,
    lwd.impulse            = lwd.impulse,
    lwd.grid               = lwd.grid,
    lwd.titer.outline      = lwd.titer.outline,
    col.grid               = col.grid,
    col.surface            = col.surface,
    col.surface.grid       = col.surface.grid,
    opacity.basemap        = opacity.basemap,
    opacity.basemap.ags    = opacity.basemap.ags,
    opacity.basemap.sr     = opacity.basemap.sr,
    opacity.surface        = opacity.surface,
    opacity.surface.grid   = opacity.surface.grid,
    shininess.surface      = shininess.surface,
    sidegrid.lwd           = sidegrid.lwd,
    sidegrid.col           = sidegrid.col,
    sidegrid.at            = sidegrid.at
  )
  
}