Plot TxpResult objects

Usage

# S4 method for class 'TxpResult,missing'
plot(
  x,
  package = c("grid", "ggplot2"),
  fills = NULL,
  showScore = TRUE,
  gp = NULL,
  vp = NULL,
  name = NULL,
  newpage = TRUE,
  ...,
  ncol = NULL,
  bgColor = "grey80",
  borderColor = "white",
  sliceBorderColor = "white",
  sliceValueColor = NULL,
  sliceLineColor = NULL,
  showMissing = TRUE,
  showCenter = TRUE
)

# S4 method for class '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
package: Character scalar, choice of "grid" or "ggplot2" for plotting ToxPi profiles
fills: Vector of colors to fill slices. Set to NULL to use default
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
ncol: Number of columns for ggplot2 ToxPi profiles
bgColor, borderColor, sliceBorderColor, sliceValueColor, sliceLineColor: Various color options when creating ggplot2 ToxPi profiles. Set to NULL for no color
showMissing: Boolean for coloring data missingness in ggplot2 ToxPi profiles
showCenter: Boolean for showing inner circle in ggplot2 ToxPi profiles. When set to False overrides showMissing
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 when using grid; called for side effect (i.e. drawing in current graphics device). Will return ggplot2 object otherwise.

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.

ToxPi profiles can also be plotted using the ggplot2 package.

Functions

plot(x = TxpResult, y = missing): Plot ToxPi diagrams
plot(x = TxpResult, y = numeric): 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[order(txpRanks(res))[1:4]])


library(ggplot2)
plot(res, package = "gg")

plot(res[order(txpRanks(res))], package = "gg", ncol = 5) +
  theme(legend.position = "bottom")


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) { # \dontrun{
tmpPdf <- tempfile()
pdf(tmpPdf)
plot(res, txpRanks(res), labels = c(10, 4, 2), pch = 16)
dev.off()
} # }