Spectra Plotting with ggplot2 Was Moved to hySpc.ggplot2 (DEPRECATED)

These ggplot2-related hyperSpec functions are deprecated and they will be removed in the next release of the package. Now functions from package hySpc.ggplot2 (link) should be used as alternatives to plot hyperSpec objects with ggplot2.

qplotspc(
  x,
  wl.range = TRUE,
  ...,
  mapping = aes_string(x = ".wavelength", y = "spc", group = ".rownames"),
  spc.nmax = hy.getOption("ggplot.spc.nmax"),
  map.lineonly = FALSE,
  debuglevel = hy.getOption("debuglevel")
)

qplotmap(
  object,
  mapping = aes_string(x = "x", y = "y", fill = "spc"),
  ...,
  func = mean,
  func.args = list(),
  map.tileonly = FALSE
)

qplotc(
  object,
  mapping = aes_string(x = "c", y = "spc"),
  ...,
  func = NULL,
  func.args = list(),
  map.pointonly = FALSE
)

qplotmixmap(object, ...)

legendright(p, l, legend.width = 8, legend.unit = "lines")

qmixtile(
  object,
  purecol = stop("pure component colors needed."),
  mapping = aes_string(x = "x", y = "y", fill = "spc"),
  ...,
  map.tileonly = FALSE
)

normalize.colrange(x, na.rm = TRUE, legend = FALSE, n = 100, ...)

normalize.range(x, na.rm = TRUE, legend = FALSE, n = 100, ...)

normalize.null(x, na.rm = TRUE, legend = FALSE, n = 100, ...)

normalize.minmax(x, min = 0, max = 1, legend = FALSE, n = 100, ...)

qmixlegend(
  x,
  purecol,
  dx = 0.33,
  ny = 100,
  labels = names(purecol),
  normalize = normalize.colrange,
  ...
)

colmix.rgb(
  x,
  purecol,
  against = 1,
  sub = TRUE,
  normalize = normalize.colrange,
  ...
)

Arguments

x	matrix with component intensities in columns
wl.range	wavelength ranges to plot
...	qmixtile: handed to colmix.rgb() qmixlegend() and colmix.rgb() hand further arguments to the normalize function
mapping	see ggplot2::geom_tile()
spc.nmax	maximum number of spectra to plot
map.lineonly	if TRUE, mapping will be handed to ggplot2::geom_line() instead of ggplot2::ggplot().
debuglevel	if > 0, additional debug output is produced
object	matrix to be plotted with mixed colour channels
func	function to summarize the wavelengths, if NULL, only the first wavelength is used
func.args	arguments to func
map.tileonly	if TRUE, mapping will be handed to ggplot2::geom_tile() instead of ggplot2::ggplot().
map.pointonly	if TRUE, mapping will be handed to ggplot2::geom_point() instead of ggplot2::ggplot().
p	plot object
l	legend object
legend.width, legend.unit	size of legend part
purecol	pure component colours, names determine legend labels
na.rm	see base::min()
legend	should a legend be produced instead of normalized values?
n	of colours to produce in legend
min	numeric with value corresponding to "lowest" colour for each column
max	numeric with value corresponding to "hightest" colour for each column
dx	width of label bar
ny	number of colours in legend
labels	component names
normalize	function to normalize the values.
against	value to mix against (for sub = TRUE only, 1 = white, 0 = black)
sub	subtractive color mixing?

Author

Claudia Beleites

Examples

qplotspc(flu)
#> Warning: Function 'qplotspc' is deprecated. 
#> Use function 'qplotspc' from package 'hySpc.ggplot2' instead.
#> https://r-hyperspec.github.io/hySpc.ggplot2

qplotmap(faux_cell[, , 1200])
#> Warning: Function 'qplotmap' is deprecated. 
#> Use function 'qplotmap' from package 'hySpc.ggplot2' instead.
#> https://r-hyperspec.github.io/hySpc.ggplot2

qplotc(flu)
#> Warning: Function 'qplotc' is deprecated. 
#> Use function 'qplotc' from package 'hySpc.ggplot2' instead.
#> https://r-hyperspec.github.io/hySpc.ggplot2
#> Warning: Intensity at first wavelengh only is used.

faux_cell <- faux_cell - spc.fit.poly.below(faux_cell)

qplotmixmap(faux_cell [, , c(800, 1200, 1500)],
  purecol = c(A = "green4", B = "yellow", C = "royalblue")
)
#> Warning: Function 'qplotmixmap' is deprecated. 
#> Use function 'qplotmixmap' from package 'hySpc.ggplot2' instead.
#> https://r-hyperspec.github.io/hySpc.ggplot2
#> Warning: Removed 300 rows containing missing values (geom_point).