hyperSpec (version 0.95)

plotc: Calibration- and Timeseries Plots, Depth-Profiles and the like

Description

plotc plots a summary value of each spectrum of a hyperSpec object over another dimension such as concentration, time, or a spatial coordinate.

Usage

plotc(object, use.c = "c", func = sum, ...,
      z = NULL, zlab = NULL, add = FALSE, plot.args = list())

Arguments

object

the hyperSpec object

use.c

the name of the column to plot against

func

function to compute the summary value from the spectra

...

further arguments to func

z

as an alternative to computing the value via func: a numeric with the respective value for each of the spectra.

zlab

label for the ordinate

add

if FALSE, a new plot is created, if TRUE the output is added to the active plot

plot.args

list with further arguments to plot and lines, respectively.

Details

If z is not given, it is calculated by apply (object, 1, func, ...).

Examples

## example 1: calibration of fluorescence 
plotc (flu)

plotc (flu[,,450], zlab = expression (I ["450 nm"] / a.u.))

calibration <- lm (spc ~ c, data = flu[,,450]$.)
summary (calibration)

conc <- list (c = seq (from = 0.04, to = 0.31, by = 0.01))
ci <- predict (calibration, newdata = conc, interval = "confidence", level = 0.999) 
matlines (conc$c, ci, col = c ("red", "#606060","#606060"), lty = 1)



## example 2: time-trace of laser emission modes
cols <- c ("black", "blue", "#008000", "red")
wl <- i2wl (laser, c(13, 17, 21, 23))

plotspc (laser, axis.args=list (x = list (at = seq (404.5, 405.8, .1))))
for (i in seq_along (wl))
   abline (v = wl[i], col = cols[i], lwd = 2)

X11()
plotc (laser[,,wl [1]], use.c = "t",
       plot.args = list (ylim = range(laser[[]]), type = "o"))
for (i in seq_along (wl)[-1]){
   plotc (laser[,,wl[i]], use.c = "t", add = TRUE,
          plot.args = list (type = "o", col = cols[i]))
}