plot.acmap {Racmacs}

Plot an antigenic map

Description

Method for plotting an antigenic map in two dimensions

Usage

## S3 method for class '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.

See Also

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