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,
  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,
  label.offset = 0,
  padding = 1,
  cex = 1,
  ...
)

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

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

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

...

additional arguments, not used

See also