Plot diagnostics for a bglmnet object

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

Usage

# S3 method for class '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)

Usage

Arguments

See also