Plot an antigenic map using the 'grid' plotting system, this is harder to edit afterwards but allows maps with custom point shapes like "EGG" and "UGLYEGG" to be plotted, or maps where point aspect or rotation has been altered.

grid.plot.acmap(
  map,
  optimization_number = 1,
  xlim = NULL,
  ylim = NULL,
  plot_ags = TRUE,
  plot_sr = TRUE,
  plot_labels = FALSE,
  plot_blobs = TRUE,
  plot_hemisphering = TRUE,
  grid.col = "grey90",
  grid.margin.col = grid.col,
  fill.alpha = 0.8,
  outline.alpha = 0.8,
  padding = 1,
  cex = 1
)

Arguments

map

The acmap to plot

optimization_number

The optimization number to plot

xlim

optional x axis limits

ylim

optional y axis limits

plot_ags

logical, should antigens be plotted

plot_sr

logical, should antigens be plotted

plot_labels

logical, should point labels be plotted

plot_blobs

logical, should stress blobs be plotted if present

plot_hemisphering

logical, should arrows be plotted to indicate hemisphering or trapped points (only for maps where checkHemisphering() has already been run)

grid.col

grid line color

grid.margin.col

grid margin color

fill.alpha

alpha for point fill

outline.alpha

alpha for point outline

padding

padding at limits of the antigenic map, ignored if xlim or ylim set explicitly

cex

point size expansion factor

See also

Other functions to view maps: RacViewer.options(), RacViewer(), export_viewer(), plot.acmap(), setLegend(), snapshotMap(), view.acmap(), view.default(), view()