Plot an antigenic map

Method for plotting an antigenic map in two dimensions

# S3 method for acmap
plot(
  x,
  optimization_number = 1,
  xlim = NULL,
  ylim = NULL,
  plot_ags = TRUE,
  plot_sr = TRUE,
  plot_labels = FALSE,
  plot_blobs = TRUE,
  point_opacity = "automatic",
  show_procrustes = TRUE,
  show_error_lines = FALSE,
  plot_stress = FALSE,
  indicate_outliers = "arrowheads",
  grid.col = "grey90",
  grid.margin.col = "grey50",
  outlier.arrow.col = grid.col,
  fill.alpha = 0.8,
  outline.alpha = 0.8,
  procrustes.lwd = 2,
  procrustes.col = "black",
  procrustes.arr.type = "triangle",
  procrustes.arr.length = 0.2,
  procrustes.arr.width = 0.15,
  label.offset = 0,
  padding = 1,
  cex = 1,
  margins = rep(0.5, 4),
  ...
)

Arguments

x: 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: should point labels be plotted, can be true, false or "antigens" or "sera"
plot_blobs: logical, should stress blobs be plotted if present
point_opacity: Either "automatic" or "fixed". "fixed" fixes point opacity to match those in ptFill() and ptOutline() and will not be altered in procrustes plots or by the fill.alpha and outline.alpha parameters.
show_procrustes: logical, should procrustes lines be shown, if present
show_error_lines: logical, should error lines be drawn
plot_stress: logical, should map stress be plotted in lower left corner
indicate_outliers: how should points outside the plotting region be indicated, either FALSE, for not shown, "arrowheads" for small arrowheads like in the viewer, or "arrows" for arrows pointing from the edge of the plot margin, default is "arrowheads".
grid.col: grid line color
grid.margin.col: grid margin color
outlier.arrow.col: outlier arrow color
fill.alpha: alpha for point fill
outline.alpha: alpha for point outline
procrustes.lwd: procrustes arrow line width
procrustes.col: procrustes arrow color
procrustes.arr.type: procrustes arrow type (see shape::Arrows())
procrustes.arr.length: procrustes arrow length (see shape::Arrows())
procrustes.arr.width: procrustes arrow width (see shape::Arrows())
label.offset: amount by which any point labels should be offset from point coordinates in fractions of a character width
padding: padding at limits of the antigenic map, ignored if xlim or ylim set explicitly
cex: point size expansion factor
margins: margins in inches for the plot, use NULL for default margins from par("mar")
...: additional arguments, not used

Value

Called for the side effect of plotting the map but invisibly returns the map object.

Arguments

Value

See also