plotspc: Plotting Spectra Plot the spectra of a `hyperSpec` object, i.e. intensity over wavelength. Instead of the intensity values of the spectra matrix summary values calculated from these may be used.

Description

This is hyperSpec's main plotting function for spectra plots.

Usually, the stacked argument of plotspc will do fine, but if you need fine control over the stacking, you may calculate the y offsets yourself.

Usage

plotspc(object, wl.range = NULL, wl.index = FALSE,
    wl.reverse = FALSE, spc.nmax = 50, func = NULL,
    func.args = list(), stacked = NULL,
    stacked.args = list(), add = FALSE, bty = "l",
    plot.args = list(), col = "black", lines.args = list(),
    xoffset = 0, yoffset = 0, nxticks = 10,
    axis.args = list(), break.args = list(),
    title.args = list(), fill = NULL, fill.col = NULL,
    border = NA, polygon.args = list(),
    zeroline = list(lty = 2, col = col))
  stacked.offsets(x, stacked = TRUE, min.zero = FALSE,
    add.factor = 0.05, add.sum = 0, .spc = NULL)

Arguments

object

the hyperSpec object

wl.range

the wavelength range to be plotted.

Either a numeric vector or a list of vectors with different wavelength ranges to be plotted separately.

The values can be either wavelengths or wavelength indices (according to wl.index).

wl.index

if TRUE, wl.range is considered to give column indices into the spectra matrix. Defaults to specifying wavelength values rather than indices.

wl.reverse

if TRUE, the wavelength axis is plotted backwards.

spc.nmax

maximal number of spectra to be plotted (to avoid accidentally plotting of large numbers of spectra).

func

a function to apply to each wavelength in order to calculate summary spectra such as mean, min, max, etc.

func.args

list with furter arguments for func

add

if TRUE, the output is added to the existing plot

bty

see par

col

see par. col might be a vector giving individual colors for the spectra.

xoffset

vector with abscissa offsets for each of the wl.ranges. If it has one element less than there are wl.ranges, 0 is padded at the beginning.

The values are interpreted as the distance along the wavelength axis that the fol

yoffset

ordinate offset values for the spectra. May be offsets to stack the spectra (stacked.offsets). Either one for all spectra, one per spectrum or one per group in stacked.

nxticks

hint how many tick marks the abscissa should have.

stacked

if not NULL, a "stacked" plot is produced, see the example. stacked may be TRUE to stack single spectra. A numeric or factor is interpreted as giving the grouping, character is interpreted as the name of the

stacked.args

a list with further arguments to stacked.offsets.

fill

if not NULL, the area between the specified spectra is filled with color col. The grouping can be given as factor or numeric, or as a character with the name of the extra data column to use. If a group contains more than

fill.col

character vector with fill color. Defaults to brightened colors from col.

border

character vector with border color. You will need to set the line color col to NA in order see the effect.

plot.args

list with further arguments to plot

axis.args

list with further arguments for axis. axis.args$x should contain arguments for plotting the abscissa, axis.args$y those for the ordinate (again as l

title.args

list with further arguments to title.

title.args may contain two lists, $x, and $y to set parameters individually for each axis.

lines.args

list with further arguments to lines.

lines.args$type defaults to "l".

break.args

list with arguments for axis.break.

polygon.args

list with further arguments to polygon which draws the filled areas.

zeroline

NA or a list with arguments abline, used to plot line (s) marking I = 0.

NA suppresses plotting of the line. The line is by default turned off if yoffset

a hyperSpec object

min.zero

if TRUE, the lesser of zero and the minimum intensity of the spectrum is used as minimum.

add.factor,add.sum

proportion and absolute amount of space that should be added.

.spc

for internal use. If given, the ranges are evaluated on .spc. However, this may change in future.

Value

plotspc invisibly returns a list with
xthe abscissa coordinates of the plotted spectral data points
ya matrix the ordinate coordinates of the plotted spectral data points
wavelengthsthe wavelengths of the plotted spectral data points
This can be used together with spc.identify.
a list containing
offsetsnumeric with the yoffset for each group in stacked
groupsnumeric with the group number for each spectrum
levelsif stacked is a factor, the levels of the groups

Details

New plots are created by plot, but the abscissa and ordinate are drawn separately by axis. Also, title is called explicitly to set up titles and axis labels. This allows fine-grained customization of the plots.

If package plotrix is available, its function axis.break is used to produce break marks for cut wavelength axes.

Empty levels of the stacking factor are dropped (as no stacking offset can be calculated in that case.)

Examples

Run this code

plotspc (flu)

## artificial example to show wavelength axis cutting
plotspc (chondro [sample (nrow (chondro), 50)],
         wl.range = list (600 ~ 650, 1000 ~ 1100, 1600 ~ 1700),
         xoffset = c (0, 300, 450))

plotspc (chondro [sample (nrow (chondro), 50)],
         wl.range = list (600 ~ 650, 1000 ~ 1100, 1600 ~ 1700),
         xoffset = c (300, 450))

## some journals publish Raman spectra backwards
plotspc (chondro [sample (nrow (chondro), 50)], wl.reverse = TRUE)

plotspc (laser[(0:4)*20+1,,], stacked = TRUE)

plotspc (laser, func = mean_pm_sd,
         col = c(NA, "red", "black"), lines.args = list (lwd = 2),
         fill = c (1, NA, 1),
         fill.col = "yellow", border = "blue",
         polygon.args = list (lty = 2, lwd = 4),
         title.args = list (xlab = expression (lambda[emission] / nm),
                            y = list(line = 3.4),
                            col.lab = "darkgreen"),
         axis.args = list (x = list (col = "magenta"), y = list (las = 1))
        )

mean.pm.sd <- aggregate (chondro, chondro$clusters, mean_pm_sd)
plot (mean.pm.sd, col = matlab.palette (3), fill = ".aggregate", stacked = ".aggregate")
mean.pm.sd <- aggregate (chondro, chondro$clusters, mean_pm_sd)

offset <- stacked.offsets (mean.pm.sd, ".aggregate")
plot (mean.pm.sd, fill.col = matlab.palette (3), fill = ".aggregate",
      stacked = ".aggregate")

plot (aggregate (chondro, chondro$clusters, mean), yoffset = offset$offsets,
      lines.args = list (lty = 2, lwd = 2), add = TRUE)

barb <- do.call (collapse, barbiturates [1:3])
plot (barb, lines.args = list (type = "h"), stacked = TRUE,
      stacked.args = list (add.factor = .2))

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