[+] Plot difference between original and reconstructed spectra

Plot difference between original (e.g., experimental) and reconstructed spectra. Function reconstructSp is used to reconstruct spectra, that are subtracted from original spectra afrterwards.

plot_spDiff(
  loadings,
  scores,
  sp,
  Title = "Difference between oginal and reconstructed spectra",
  color = if (".color" %in% names(sp$..)) sp$.color else "blue3",
  stacked = if ("ID" %in% names(sp$..)) sp$ID else NULL,
  spc.nmax = 2000,
  ...
)

Arguments

loadings

Components' spectra (loadings) as a hyperSpec object.

scores

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

sp

hyperSpec object.

Title

The main title for the plot.

color

see par col. Might be a vector giving individual colors for the spectra. Default values: vector in sp$.color, if does not exist, "tan3" is used as a default color.

stacked

if not NULL, a "stacked" plot is produced. stacked may be TRUE to stack single spectra. A numeric or factor is be interpreted as giving the grouping, character is interpreted as the name of the extra data column that holds the groups. Default stacking is by sp$ID, and NULL if this variable is missing.

...

Other parameters to be passed to function plotspc.

Value

A plot of calculated difference between expected (original) and reconstructed spectra. (Drawn with R package graphics).

Note

Function plotspc is used to make a plot. R base plotting system annotations can be used to enhance the plot.

See also

Other spHelper plots: check_palette(), layer_spRangeMean(), plot_colors(), plot_hyPalette(), plot_spCompare(), plot_spDistribution(), qplot_confusion(), qplot_crosstab(), qplot_infoDim(), 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(), qplot_infoDim(), qplot_kAmp(), qplot_kSp(), qplot_spc(), reconstructSp(), sortLoadings(), unipeak(), whichOutlier()

Author

Vilmantas Gegzna

Examples

plot_spDiff(Loadings2, Scores2[1:10,,], Spectra2[1:10,,], stacked = TRUE)
#> Warning: Function 'plotspc' is deprecated. 
#> Use function 'plot_spc' instead.