qplot_kSp | R Documentation |
Plot spectroscopic curves in different colors.
Functions qplot_kSp
, qplot_kSpFacets
are designed
to plot spectra of spectral components
(a.k.a. loadings), extracted in principal component analysis
(e.g., princomp
), variaus matrix factorization
methods (e.g., nmf
)) and some other dimension
reduction methods.
The function qplot_sp
is convenient for all spectroscopic
curves as uses no fill.
qplot_kSp(
loadings,
Title = "Components",
xLabel = labels(loadings, ".wavelength"),
yLabel = labels(loadings, "spc"),
by = "cNames",
palette = hyGet_palette(loadings),
legendName = FALSE,
filled = TRUE,
normalize = FALSE,
facets = FALSE,
subTitle = NULL,
names.in = NULL,
line_size = 1
)
qplot_kSpFacets(
...,
Title = "Components (stacked)",
normalize = "auto",
facets = TRUE
)
qplot_sp(..., Title = NULL, filled = FALSE, line_size = 0.5)
loadings |
Components' spectra (loadings) as a |
Title |
The main title for the plot. |
xLabel |
A label for abscisa (x) axis. |
yLabel |
A label for ordinate (y) axis. |
by |
A name of variable in |
legendName |
A name of a legend. Possible entries:
|
filled |
Logical. If |
normalize |
A flag that indicates whether components should be normalized before plotting. Possible selections:
|
facets |
A logical flag. If |
subTitle |
The second line of title, which will be smaller and and in italics. |
names.in |
DEPRECATED. Use |
... |
(The same parameters as above). |
qplot_kSp
plots spectra on one graph.
qplot_kSpFacets
plots spectra on separate graphs (facets).
A ggplot
object.
More details in package ggplot2.
Before using as an argument loadings
,
a matrix of components/loadings (loadings
) must be treated
with function decomposition
(or equivalent)
which converts it to hyperSpec
object.
Vilmantas Gegzna
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_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_infoDim()
,
qplot_kAmp()
,
qplot_spc()
,
reconstructSp()
,
sortLoadings()
,
unipeak()
,
whichOutlier()
qplot_kSp(Loadings2)
data(flu, package = "hyperSpec")
qplot_kSpFacets(flu, Title = "Flu dataset")
qplot_kSpFacets(flu, Title = "Flu dataset", normalize = 1)
qplot_kSpFacets(flu, Title = "Flu dataset", normalize = FALSE)
qplot_kSpFacets(flu, Title = "Flu dataset", normalize = -1)
## Remove fill -----------------------------------------------------------------
qplot_kSp(flu, filled = FALSE)
qplot_sp(flu)
## Name of a legend ------------------------------------------------------------
flu$c2 <- as.factor(flu$c)
qplot_sp(flu, Title = "Flu dataset", by = 'c2', legendName = FALSE)
qplot_sp(flu, Title = "Flu dataset", by = 'c2', legendName = TRUE)
qplot_sp(flu, Title = "Flu dataset", by = 'c2', legendName = "Concentration")
## Example of line color transitions -------------------------------------------
qplot_sp(laser)
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