Plot bird flux

Plot bird flux

Usage

plot_flux(
  flux,
  bf,
  subset = NULL,
  limits = NULL,
  dynamic_scale = FALSE,
  coast_linewidth = 0.25,
  coast_color = gray(0.5),
  gradient_colors = NULL,
  title = species(bf),
  value_label = "Flux",
  transform = "identity"
)

Arguments

flux

A flux object as created by calc_flux(format = "dataframe")

bf

A BirdFlow object

subset

A subset of the transitions in flux to plot, can be a logical vector of the same length as the number of transitions in flux; a numeric index of transitions in flux, or a subset of the transition names in flux.

limits

Two numbers representing the range in flux values to display. Values outside of this range will be truncated to the range. With the default of NULL the entire range is plotted.

dynamic_scale

If TRUE then the range of the data in each transition is mapped to the color palette. This makes it easier to see the variation within a single transition but results in an inconsistent scale among transitions.

coast_linewidth

The line width used to plot the coast. Set to NULL to skip plotting the coastline.

coast_color

The color used to plot the coastline, or NULL to skip plotting the coastline.

gradient_colors

The colors palette used to represent the flux intensity.

title

The plot title

value_label

The label for the flux values.

transform

A transformation to apply to the color scaling. "identity", and "sqrt" are recommended. If "log" is used zeros will be replaced with 1/2 the smallest non-zero value prior to transforming. Legend will still reflect the original values. Passed to ggplot2::scale_color_gradientn().

Value

plot_flux returns a ggplot2 object. It can be displayed with print().

Examples

if (FALSE) { # \dontrun{
bf <- BirdFlowModels::amewoo
flux <- calc_flux(bf)

plot_flux(flux, bf)

animate_flux(flux, bf)
} # }