CalibrationPlot {sharp}

Calibration plot

Description

Creates a plot showing the stability score as a function of the parameter(s) controlling the level of sparsity in the underlying feature selection algorithm and/or the threshold in selection proportions. See examples in VariableSelection, GraphicalModel, Clustering and BiSelection.

Usage

CalibrationPlot(
  stability,
  block_id = NULL,
  col = NULL,
  pch = 19,
  cex = 0.7,
  xlim = NULL,
  ylim = NULL,
  bty = "o",
  lines = TRUE,
  lty = 3,
  lwd = 2,
  show_argmax = TRUE,
  show_pix = FALSE,
  show_piy = FALSE,
  offset = 0.3,
  legend = TRUE,
  legend_length = NULL,
  legend_range = NULL,
  ncol = 1,
  xlab = NULL,
  ylab = NULL,
  zlab = expression(italic(q)),
  xlas = 2,
  ylas = NULL,
  zlas = 2,
  cex.lab = 1.5,
  cex.axis = 1,
  cex.legend = 1.2,
  xgrid = FALSE,
  ygrid = FALSE,
  params = c("ny", "alphay", "nx", "alphax")
)

Arguments

stability

output of VariableSelection, GraphicalModel or BiSelection.

block_id

ID of the block to visualise. Only used for multi-block stability selection graphical models. If block_id=NULL, all blocks are represented in separate panels.

col

vector of colours.

pch

type of point, as in points.

cex

size of point.

xlim

displayed range along the x-axis. Only used if stability is the output of BiSelection.

ylim

displayed range along the y-axis. Only used if stability is the output of BiSelection.

bty

character string indicating if the box around the plot should be drawn. Possible values include: "o" (default, the box is drawn), or "n" (no box).

lines

logical indicating if the points should be linked by lines. Only used if stability is the output of BiSelection or Clustering.

lty

line type, as in par. Only used if stability is the output of BiSelection.

lwd

line width, as in par. Only used if stability is the output of BiSelection.

show_argmax

logical indicating if the calibrated parameter(s) should be indicated by lines.

show_pix

logical indicating if the calibrated threshold in selection proportion in X should be written for each point. Only used if stability is the output of BiSelection.

show_piy

logical indicating if the calibrated threshold in selection proportion in Y should be written for each point. Only used if stability is the output of BiSelection with penalisation of the outcomes.

offset

distance between the point and the text, as in text. Only used if show_pix=TRUE or show_piy=TRUE.

legend

logical indicating if the legend should be included.

legend_length

length of the colour bar. Only used if stability is the output of VariableSelection or GraphicalModel.

legend_range

range of the colour bar. Only used if stability is the output of VariableSelection or GraphicalModel.

ncol

integer indicating the number of columns in the legend.

xlab

label of the x-axis.

ylab

label of the y-axis.

zlab

label of the z-axis. Only used if stability is the output of VariableSelection or GraphicalModel.

xlas

orientation of labels on the x-axis, as las in par.

ylas

orientation of labels on the y-axis, as las in par.

zlas

orientation of labels on the z-axis, as las in par.

cex.lab

font size for labels.

cex.axis

font size for axes.

cex.legend

font size for text legend entries.

xgrid

logical indicating if a vertical grid should be drawn. Only used if stability is the output of BiSelection.

ygrid

logical indicating if a horizontal grid should be drawn. Only used if stability is the output of BiSelection.

params

vector of possible parameters if stability is of class bi_selection. The order of these parameters defines the order in which they are represented. Only used if stability is the output of BiSelection.

Value

A calibration plot.

See Also

VariableSelection, GraphicalModel, Clustering, BiSelection