Plot diagnostics for a bglmnet object

A plot method to visualise the results of a bglmnet object.

# S3 method for bglmnet
plot(
  x,
  highlight,
  interactive = FALSE,
  classic = NULL,
  tag = NULL,
  shiny = FALSE,
  which = c("vip", "boot", "boot_size"),
  width = 800,
  height = 400,
  fontSize = 12,
  left = 50,
  top = 30,
  chartWidth = "60%",
  chartHeight = "80%",
  axisTitlesPosition = "out",
  dataOpacity = 0.5,
  options = NULL,
  hAxis.logScale = TRUE,
  ylim,
  text = FALSE,
  backgroundColor = "transparent",
  legend.position = "right",
  jitterk = 0.1,
  srt = 45,
  max.circle = 15,
  min.prob = 0.1,
  ...
)

Arguments

x	`bglmnet` object, the result of `bglmnet`
highlight	the name of a variable that will be highlighted.
interactive	logical. If `interactive=TRUE` a googleVis plot is provided instead of the base graphics plot. Default is `interactive=FALSE`.
classic	logical. Depricated. If `classic=TRUE` a base graphics plot is provided instead of a googleVis plot. For now specifying `classic` will overwrite the default `interactive` behaviour, though this is likely to be removed in the future.
tag	Default NULL. Name tag of the objects to be extracted from a gvis (googleVis) object. The default tag for is NULL, which will result in R opening a browser window. Setting `tag='chart'` or setting `options(gvis.plot.tag='chart')` is useful when googleVis is used in scripts, like knitr or rmarkdown.
shiny	Default FALSE. Set to TRUE when using in a shiny interface.
which	a vector specifying the plots to be output. Variable inclusion type plots `which = "vip"` or plots where the size of the point representing each model is proportional to selection probabilities by model size `which = "boot_size"` or by penalty paramter `which = "boot"`.
width	Width of the googleVis chart canvas area, in pixels. Default: 800.
height	Height of the googleVis chart canvas area, in pixels. Default: 400.
fontSize	font size used in googleVis chart. Default: 12.
left	space at left of chart (pixels?). Default: "50".
top	space at top of chart (pixels?). Default: "30".
chartWidth	googleVis chart area width. A simple number is a value in pixels; a string containing a number followed by `%` is a percentage. Default: `"60%"`
chartHeight	googleVis chart area height. A simple number is a value in pixels; a string containing a number followed by `%` is a percentage. Default: `"80%"`
axisTitlesPosition	Where to place the googleVis axis titles, compared to the chart area. Supported values: "in" - Draw the axis titles inside the the chart area. "out" - Draw the axis titles outside the chart area. "none" - Omit the axis titles.
dataOpacity	The transparency of googleVis data points, with 1.0 being completely opaque and 0.0 fully transparent.
options	a list to be passed to the googleVis function giving complete control over the output. Specifying a value for `options` overwrites all other plotting variables.
hAxis.logScale	logical, whether or not to use a log scale on the horizontal axis. Default = TRUE.
ylim	the y limits of the `which="boot"` plots.
text	logical, whether or not to add text labels to classic boot plot. Default = `FALSE`.
backgroundColor	The background colour for the main area of the chart. A simple HTML color string, for example: 'red' or '#00cc00'. Default: 'transparent'
legend.position	the postion of the legend for classic plots. Default `legend.position="right"` alternatives include `legend.position="top"` and `legend.position="bottom"`
jitterk	amount of jittering of the model size in the lvk and boot plots. Default = 0.1.
srt	when `text=TRUE`, the angle of rotation for the text labels. Default = 45.
max.circle	determines the maximum circle size. Default = 15.
min.prob	lower bound on the probability of a model being selected. If a model has a selection probability lower than `min.prob` it will not be plotted.
...	further arguments (currently unused)

Arguments

See also