tcplPlot: #—————— Generic Plotting Function for tcpl

In tcpl: ToxCast Data Analysis Pipeline

#——————————————————————————- Generic Plotting Function for tcpl

Description

tcplPlot queries the tcpl databases and returns a plot for the given level and data type.

Usage

tcplPlot(
  dat = NULL,
  type = "mc",
  fld = "m4id",
  val = NULL,
  compare.val = NULL,
  by = NULL,
  output = c("console", "pdf", "png", "jpg", "svg", "tiff"),
  fileprefix = paste0("tcplPlot_", Sys.Date()),
  multi = NULL,
  verbose = FALSE,
  nrow = NULL,
  ncol = NULL,
  dpi = 600,
  flags = FALSE,
  yuniform = FALSE,
  yrange = c(NA, NA)
)

Arguments

dat	data.table containing plot-prepared data, used for stand-alone (non-ToxCast data like other tcplfit2-fit data) or advanced plotting (generating comparison plots across multiple database configurations) and not required. See tcplPlotLoadData.
type	Character of length 1, the data type, "sc" or "mc".
fld	Character, the field(s) to query on.
val	List, vectors of values for each field to query on. Must be in the same order as 'fld'.
compare.val	List, vectors of values for each field to query on to compare with val. Must be in the same order as 'fld'. Must have the same length as val (1:1 comparison). Must be set to compare plots; otherwise leave NULL
by	Parameter to divide files into e.g. "aeid".
output	How should the plot be presented. To work with the plot in environment, use "ggplot"; to interact with the plot in application, use "console"; or to save as a file type, use "pdf", "jpg", "png", "svg", or "tiff".
fileprefix	Prefix of file when saving.
multi	Boolean, by default TRUE for "pdf". If multi is TRUE, output by default 4 plots per page for 'verbose' = TRUE and 6 plots per page for 'verbose' = FALSE.
verbose	Boolean, by default FALSE. If TRUE, a table with fitting parameters is included with the plot.
nrow	Integer, number of rows in multiplot. By default 2.
ncol	Integer, number of columns in multiplot. By default 3, 2 if verbose.
dpi	Integer, image print resolution. By default 600.
flags	Boolean, by default FALSE. If TRUE, level 6 flags are displayed below annotations on plot
yuniform	Boolean, by default FALSE. If TRUE, all plots will have uniform y axis scaling, automatically determined.
yrange	Integer of length 2, for directly setting the y-axis range, c(<min>,<max>). By default, c(NA,NA).

Details

The data type can be either 'mc' for multiple concentration data, or 'sc' for single concentration data. Multiple concentration data will be loaded into the 'mc' tables, whereas the single concentration will be loaded into the 'sc' tables.

Leaving fld NULL will return all data.

Examples

## Not run: 
tcplPlot(fld = "m4id", val = c(18609966)) ## Create a level 4 plot

## End(Not run)

tcpl documentation built on Oct. 10, 2024, 1:07 a.m.