qplot_infoDim: [+] Scree plot with indicated information dimension (ggplot2)

In GegznaV/spHelper: Extension of Package `hyperSpec` and Various Convenience Functions

[+] Scree plot with indicated information dimension (ggplot2)

Description

Plot a screeplot and with indicated information dimension.

Usage

qplot_infoDim(
  obj,
  n.comp.SHOW = 20,
  selected = NA,
  Title = "Scree Plot",
  y.log = TRUE,
  show.legend = TRUE,
  legend.position = c(0.8, 0.8),
  ggtheme = theme_bw()
)

qplot_screeplot(obj, ...)

qplot_scree(obj, ...)

Arguments

obj	Either a matrix (rows = observations, columns = variables; to be passed to infoDim) or an obj (a list) generated by function infoDim.
n.comp.SHOW	A number of components to show on x axis, default is 20. This number is corrected if (a) vector of eigenvalues is smaller than 20 or (b) information dimension is higher than 15.
selected	A number of components sellected, will be plotted as a separate vertical line (optional parameter).
Title	The main title of the plot.
y.log	Logical. If TRUE (default) the scale of y axis is logarythmic.
show.legend	Logical. If TRUE (default) the legend is displayed.
legend.position	the position of the legend ("none", "left", "right", "bottom", "top", or two-element numeric vector).
ggtheme	A function of ggplot2 theme to apply (e.g.: ggtheme). Default is theme_bw().
...	(The same parameters as above).

Value

A scree plot : plot which helps to determine the number of nenessary components (e.g. for PCA).
(A "ggplot" object.)

Note

http://www.originlab.com/doc

See Also

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

Other component analysis / factorisation related functions in spHelper: getScores(), infoDim(), plot_spDiff(), qplot_kAmp(), qplot_kSp(), qplot_spc(), reconstructSp(), sortLoadings(), unipeak(), whichOutlier()

Other information dimension functions: infoDim()

Examples

 data(Spectra2, package ="spHelper")
 qplot_infoDim(Spectra2)

# ------------------------------------------------------
 my_matrix <- matrix(rexp(200, rate=.1), ncol=20)
 my_result <- infoDim(my_matrix)

 # Investigate the result
 str(my_result)
 my_result$exactDim
 my_result$dim

 #Plot
 my_plot <- qplot_infoDim(my_result)
 my_plot


qplot_infoDim(my_matrix)

GegznaV/spHelper documentation built on April 16, 2023, 1:42 p.m.