plot.int.lsbclust {lsbclust}

Plot Method for Class 'int.lsbclust'

Description

Two-dimensional plot method for object of class 'int.lsbclust' as output by int.lsbclust.

Usage

## S3 method for class 'int.lsbclust'
plot(x, which = seq_len(nclust),
  plot.type = c("biplots", "means", "estimates"), segments = NULL,
  biplot.axes = TRUE, nmarkers = 5, alpha = NULL,
  check.alpha = TRUE, fix.alpha = FALSE, probs = 0,
  arrange = FALSE, fix.limits = TRUE, limit.exp = 1.05,
  lambda.scale = TRUE, procrustes.rotation = x$fixed == "none",
  fix.lambda = FALSE, labs.grey = TRUE, label.0 = FALSE,
  tick.length = 0.0075 * diff(lims), axis.col = "grey60",
  label.size = 3, axis.size = 0.25, axis.title.size = 4,
  draw.axis = NULL, points.col = list(rows = "red", columns = "blue2"),
  offset.tick.labels = 3.5, offset.axis.title = list(rows = 0.015 *
  max(nchar(rnms)), columns = 0.015 * max(nchar(cnms))),
  axis.arrow = grid::arrow(angle = 20, length = grid::unit(0.0175,
  "npc")), ...)

Arguments

x

An object of class int.lsbclust.

which

A vector indicating which item segments to plot.

plot.type

Character string giving the type of plots to produce: either "biplots" for the biplots approximating the cluster means, "means" for level plots of the cluster means themselves or "estimates" for level plots of the low-rank approximations of the cluster means (as represented in the biplots).

segments

A logical vector with two elements, indicating whether the rows and columns should be plotted as line segments or not.

biplot.axes

A logical indicating whether to plot calibrated biplot axes for the line segments indicated in segments or not.

nmarkers

Either a single integer giving the number of desired markers per biplot axis for all axes, or a named list. This is passed as the argument n to pretty. See Details for information on the list option.

alpha

Numeric value in [0, 1] which determines how the singular values are distributed between rows and columns. It will trigger a recomputation of the updates if it does not correspond to the value used when fitting the model. Do not confuse this with the term "alpha" used in the context of colour transparency.

check.alpha

Logical indicating whether to look for a better alpha. This is only used when alpha = NULL is used. Do not confuse this with the term "alpha" used in the context of colour transparency.

fix.alpha

Logical indicating whether to fix alpha across all clusters or not when fixed == "none". Do not confuse this with the term "alpha" used in the context of colour transparency.

probs

Argument passed to quantile to determine the alpha value. The corresponding quantile of the distances of all points in the biplots to the origin will be used to determine alpha in case check.alpha = TRUE.

arrange

Logical indicating whether to arrange the plots side-by-side via grid.arrange or not.

fix.limits

Logical indicating whether biplot x- and y-limits must be fixed across clusters or not. Note that this is automatically set to TRUE when fixed == "rows" or fixed == "columns". When limits are fixed, the axis calibrations are also turned off.

limit.exp

A numeric expansion factor applied multiplicatively to the plot limits, but only when fixed equals "rows" or "columns".

lambda.scale

Logical indicating whether to apply lambda scaling to the coordinates or not. If true, the scaling is done such that the average squared distance to the origin is equal for the row and column coordinates.

procrustes.rotation

Logical indicating whether to do Procrustes rotations so that the location of the axes indicated as segments (see argument segments) are similar across configurations.

fix.lambda

Logical indicating whether to fix lambda across all clusters or not.

labs.grey

Logical indicating whether to apply greying to the text labels are well.

label.0

Logical indicating whether to label the origin or not.

tick.length

The required tick length as a unit object. It defaults to a propoprtion of the width of the plot region (through lazy evaluation).

axis.col

The colour of the biplot axes.

label.size

The size of the labels for the markers on the biplot axes.

axis.size

Line size for biplot axes.

axis.title.size

Size of biplot axis titles.

draw.axis

A list with up to two components which must be named "rows" and "columns". Each element contains a vector indicating which biplot axes should be drawn. The vectors can be character vectors containing the names of the axes to be drawn, numeric vectors containing indices indicating which axes to draw, or logical vectors indicating which biplot axes to draw. In case of the default value NULL, the elements of segments are used for the "rows" and "columns" entries.

points.col

A named list containing the colours to use for plotting the sets of points. The elements "rows" and "columns" contain vectors giving the colours for the points. Single element vectors are recycled across the different points, otherwise the vectors must be of the appropriate length.

offset.tick.labels

A numeric value giving the offset factor of the biplot axis marker labels from their respective tick marks. Higher (lower) values lead to labels being further from (nearer to) their respective tick marks.

offset.axis.title

A names list of (up to) two numeric values giving the fixed length offset of the biplot axis title label from the end of the axis segment. The two elements must have names "rows" and code"columns".

axis.arrow

An arrow object to be used for the endpoints of biplot axis segment lines. This is passed to geom_segment.

...

Additional arguments passed to theme.

Details

In case nmarkers is a list, it can have up to two elements. These are required to be named "rows" and/or "columns", otherwise an error will be thrown. The elements of the list contains either single numeric values each or numeric vectors of the appropriate lengths indicating the n argument passed to pretty.

In some cases, the row and/or column fit values can contain non-finite values. If that occurs, colour transparency cannot and will not be used for that particular element (and this can vary between clusters). This relates to the alpha parameter in the plotting routines.