Plot TxpResult objects

Usage

# S4 method for TxpResult,missing
plot(
  x,
  fills = NULL,
  showScore = TRUE,
  gp = NULL,
  vp = NULL,
  name = NULL,
  newpage = TRUE,
  ...
)

# S4 method for TxpResult,numeric
plot(
  x,
  y,
  labels = NULL,
  newpage = TRUE,
  margins = c(4, 0, 1, 1),
  name = NULL,
  gp = NULL,
  vp = NULL,
  ...
)

Arguments

x: TxpResult object
fills: Vector of colors to fill slices
showScore: Logical scalar, overall score printed below the name when TRUE
gp, vp, name: Passed to grid::frameGrob when creating the plotting area
newpage: Logical scalar, grid::grid.newpage called prior to plotting when TRUE
...: Passed to pieGridGrob when plotting ToxPi and to pointsGrob when plotting ranks
y: Rank vector, i.e. txpRanks(x)
labels: Integer vector, indices of x to label in the rank plot
margins: Passed to grid::plotViewport; only affects the scatterplot region margins

Value

No return value; called for side effect (i.e. drawing in current graphics device.)

Details

It is strongly recommended to use a specific device (e.g., grDevices::png, grDevices::pdf) when creating rank plots. Using a GUI device will likely lead to inaccurate labeling, and any changes to the device size WILL lead to inaccurate labeling.

The plotting is built on the grid::grid-package, and can be adjusted or edited as such.

If the labels are running of the device, the top or bottom margins can be increased with the margins parameter.

Functions

plot,TxpResult,missing-method: Plot ToxPi diagrams
plot,TxpResult,numeric-method: Plot ToxPi ranks

Examples

## Load example dataset & model; see ?TxpModel for building model objects
data(txp_example_input, package = "toxpiR")
data(txp_example_model, package = "toxpiR")

## Calculate scores for single model; returns TxpResult object
res <- txpCalculateScores(model = txp_example_model, 
                          input = txp_example_input, 
                          id.var = "name")

library(grid)
plot(res)


plot(res, txpRanks(res))

plot(res, txpRanks(res), pch = 16, size = unit(0.75, "char"))


## Will likely make inaccurate labels within a GUI, e.g. RStudio
## use png, pdf, etc. to get accurate labels
if (FALSE) {
tmpPdf <- tempfile()
pdf(tmpPdf)
plot(res, txpRanks(res), labels = c(10, 4, 2), pch = 16)
dev.off()
}