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"