[!!!] Proximity plot created using multi-dimensiolal scaling (MDS)

Plot a 2D scatterplot that represents multidimensionally scaled data.

qplot_prediction(
  scores,
  Prediction,
  Reference,
  xLabel = paste("Projection", xproj),
  yLabel = paste("Projection", yproj),
  Title = "Proximity of Groups",
  subTitle = NULL,
  palette = hyGet_palette(scores),
  type = c("Prediction", "Reference"),
  stat = c("chull", "ellipse", "none"),
  type.stat = type,
  MDS = c("metric", "isoMDS"),
  plot.scatter = TRUE,
  alpha = 0.5,
  k = 2,
  xproj = 1,
  yproj = 2
)

qplot_proximity(
  scores,
  by,
  xLabel = paste("Projection", xproj),
  yLabel = paste("Projection", yproj),
  Title = "Proximity of Groups",
  subTitle = NULL,
  palette = hyGet_palette(scores),
  stat = c("chull", "ellipse", "none"),
  MDS = c("metric", "isoMDS"),
  plot.scatter = TRUE,
  alpha = 0.5,
  k = 2,
  xproj = 1,
  yproj = 2
)

Arguments

scores

Components' amplitudes (scores) as either a matrix or a hyperSpec object.

Prediction

Predicted groups. Either a variable name or a vector.

Reference

Reference grpups. Either a variable name or a vector.

xLabel

A label for abscisa (x) axis.

yLabel

A label for ordinate (y) axis.

Title

The main title for the plot.

subTitle

The second line of title, which will be smaller and and in italics.

palette

A color palete to be used. Default is `ggplot2` default palette.

type

A type of data for scatterplot: either "prediction" (default) or "reference".

stat

A statistic to be added, either "chull" - convex hull (default), "ellipse" or "none"

type.stat

A type of data for stat: either "prediction" (default) or "reference".

MDS

A type of Multi-Dimensional Scaling.

plot.scatter

Logical. If true (default), scatterplot (`geom_point`)is plotted.

alpha

Transperency of points.

k

The desired dimension for the solution, passed to cmdscale.

xproj, yproj

An integer: a number of MDS projection to plot on x, y axis (respectively).

by

A grouping variable

Value

A ggplot object. More details in package ggplot2.

See also

Other spHelper plots: check_palette(), layer_spRangeMean(), plot_colors(), plot_hyPalette(), plot_spCompare(), plot_spDiff(), plot_spDistribution(), qplot_confusion(), qplot_crosstab(), qplot_infoDim(), qplot_kAmp(), qplot_kSp(), qplot_spRangeCenter(), qplot_spRangeMedian(), qplot_spStat(), qplot_spc(), rmExpr(), rm_stripes(), stat_chull()

Author

Vilmantas Gegzna

Examples

# Examples with a `hyperSpec` object:

data(Scores2)
Scores2$Prediction <- sample(Scores2$gr)
Scores2 <- hyAdd_color(sp = Scores2, by = "gr", palette = c("tan3", "green4","skyblue"))

qplot_prediction(Scores2,Prediction = "Prediction", Reference = "gr")

qplot_prediction(Scores2,Prediction = "Prediction", Reference = "gr", type = "ref")


qplot_prediction(Scores2,"Prediction","gr", type.stat = "ref", MDS = "isoMDS")



sc <- Scores2[,,c(1,3),wl.index = TRUE]


qplot_prediction(sc,"Prediction","gr", type = "reference")

qplot_prediction(sc,"Prediction","gr", type = "prediction")

qplot_prediction(sc,"Prediction","gr", type = "prediction", type.stat = "ref")

qplot_prediction(sc,"Prediction","gr", type = "prediction", type.stat = "ref",stat ="ellipse")



sc <- Scores2[,,c(1,2),wl.index = TRUE]
sc <- hyAdd_color(sp = sc , by = "class", palette = c("tan3", "green4","skyblue","violet"))
sc$ID <- rownames(sc)

qplot_proximity(sc, "class")
#> Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
#> of ggplot2 3.3.4.
#> ℹ The deprecated feature was likely used in the spHelper package.
#>   Please report the issue to the authors.

qplot_proximity(sc, "class",  plot.scatter = FALSE) + geom_text(aes(label = sc$ID))