TxpResult-plot {toxpiR}

Plot TxpResult objects

Description

Plot TxpResult objects

Usage

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

## S4 method for signature '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

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.

Value

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

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
## Not run: 
tmpPdf <- tempfile()
pdf(tmpPdf)
plot(res, txpRanks(res), labels = c(10, 4, 2), pch = 16)
dev.off()

## End(Not run)