CalibrationPlot: 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")
)

Value

A calibration plot.

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.

Description

Usage

Value

Arguments

See Also