Plot an antigenic map using the grid system

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

Arguments

See also