plot.chemSigSelect {RFPM}

Plot method for 'chemSigSelect'

Description

The plot method for 'chemSigSelect' objects

Usage

## S3 method for class 'chemSigSelect'
plot(
  x,
  paramList = NULL,
  type = c("boxplot", "ecdf", "density"),
  logAxes = TRUE,
  ...
)

Arguments

x

chemSigSelect class object

paramList

character vector of column names of chemical concentration variables in data; values will be inherited from x if not specified

type

character vector indicating the type of plot to generate (see Details; default = c("boxplot", "ecdf", "density"))

logAxes

logical value; whether axes should be projected in log-space (default = TRUE)

...

additional arguments passed to plot. The user currently has limited capacity to change graphical parameters.

Details

plot.chemSigSelect is a class-specific plotting function that generates boxplots, empirical cumulative density functions, or kernel density plots comparing the Hit == TRUE and Hit == FALSE subsets for all chemicals in paramList. By default, all plot types are generated, but type can be changed to generate specific plot types. The available types are specified by "type = boxplot", "type = ecdf", and "type = density", though character inputs are flexible; for example, other reasonable versions of these types include "Boxplot" and "ECDF". Note that because boxplot, plot.ecdf, and plot.density functions use plotting arguments in different ways, supplying user-defined plotting arguments may cause unintended changes (or possibly errors or warnings) when plotting multiple types. For that reason, we recommend that the user select a specific plot type (using the type argument) before adjusting plot arguments (via ...) that apply to that type. Moreover, many of the plotting arguments are specified by plot.chemSigSelect and, therefore, cannot be adjusted by the user. These include but are not limited to parameters like col and lwd.

Value

base graphics

See Also

chemSigSelect, boxplot, plot.ecdf, plot.density

Examples

x <- chemSigSelect(data = h.tristate, 
    paramList = c("Cd", "Cu", "Fe", "Mn", "Ni", "Pb", "Zn"))
plot(x, type = "boxplot")