plot_environment: Plot spatial distribution of compounds

In Waschina/Eutropia: Agent-based modelling of microbial communities in time and continuous µ-meter-scale space

Plot spatial distribution of compounds

Description

Plots the spatial distribution of compound concentrations in a heatmap.

Usage

plot_environment(
  object,
  compounds,
  compound.names = NULL,
  xlim = NULL,
  ylim = NULL,
  iter = NULL,
  scalebar.color = "white",
  layer = 0,
  gradient.limits = NULL,
  gradient.option = "viridis",
  incl.timestamp = TRUE,
  legend.position = "right"
)

Arguments

object	S4-object of type growthSimulation.
compounds	Character string of compound ids to plot
compound.names	Character string of compound names that should be displayed as facet header instead of compound names from the simulation object.
xlim	Numeric vector of length 2 specifying the limits (left and right) for x axis; i.e. the horizontal dimension.
ylim	Numeric vector of length 2 specifying the limits (top and bottom) for y axis; i.e. the vertical dimension.
iter	Positive integer number of the simulation step/iteration to plot the distribution. Works only if the respective metabolite concentrations were prior recorded (see run_simulation). If 'NULL', current distribution of compound concentrations.
scalebar.color	Color of the scale bar and its annotation. Default: "white".
layer	Positive integer, specifying which layer (z-dimension) to plot. Default: 0 (base plane).
gradient.limits	Numeric vector of length 2 specifying the concentration range that is spanned by the color gradient.
gradient.option	Character string indicating the colormap to be used for visualizing metabolite concentrations. Please refer to scale_colour_viridis_d so see possible options.
incl.timestamp	Boolean indicating whether a timestamp should be included in the plot. Default: TRUE
legend.position	The position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector), as handled in ggplot2. Default: "right"

Value

A ggplot

Waschina/Eutropia documentation built on Jan. 4, 2023, 12:42 p.m.