plotsp {rchemo}

Plotting spectra

Description

plotsp plots lines corresponding to the row observations (e.g. spectra) of a data set.

plotsp1 plots only one observation per plot (e.g. spectrum by spectrum) by scrolling the rows. After running a plotsp1 command, the plots are printed successively by pushing the R console "entry button", and stopped by entering any character in the R console.

Usage

plotsp(X,
  type = "l", col = NULL, zeroes = FALSE, labels = FALSE, 
  add = FALSE,
  ...)

plotsp1(X, col = NULL, zeroes = FALSE, ...)

Arguments

X

Data (n, p) to plot.

type

1-character string giving the type of plot desired. Default value to "l" (lines). See plot.default for other options.

col

A color, or a vector of colors (of length n), defining the color(s) of the lines representing the rows.

zeroes

Logical indicationg if an horizontal line is drawn at coordonates (0, 0) (Default to FALSE).

labels

Logical indicating if the row names of X are plotted (default to FALSE).

add

Logical defining if the frame of the plot is plotted (add = FALSE; default) or not (add = TRUE). This allows to add new observations to a plot without red-building the frame.

...

Other arguments to pass in functions plot or lines

.

Value

A plot (see examples).

Note

For the first example, see ?hcl.colors and ?hcl.pals, and try with col <- hcl.colors(n = n, alpha = 1, rev = FALSE, palette = "Green-Orange") col <- terrain.colors(n, rev = FALSE) col <- rainbow(n, rev = FALSE, alpha = .2)

The second example is with plotsp1 (Scrolling plot of PCA loadings). After running the code, type Enter in the R console for starting the scrolling, and type any character in the R console

Examples

## EXAMPLE 1

data(cassav)

X <- cassav$Xtest
n <- nrow(X)

plotsp(X)
plotsp(X, col = "grey")
plotsp(X, col = "lightblue", 
  xlim = c(500, 1500),
  xlab = "Wawelength (nm)", ylab = "Absorbance")

col <- hcl.colors(n = n, alpha = 1, rev = FALSE, palette = "Grays")
plotsp(X, col = col)

plotsp(X, col = "grey")
plotsp(X[23, , drop = FALSE], lwd = 2, add = TRUE)
plotsp(X[c(23, 16), ], lwd = 2, add = TRUE)

plotsp(X[5, , drop = FALSE], labels = TRUE)

plotsp(X[c(5, 61), ], labels = TRUE)

col <- hcl.colors(n = n, alpha = 1, rev = FALSE, palette = "Grays")
plotsp(X, col = col)
plotsp(X[5, , drop = FALSE], col = "red", lwd = 2, add = TRUE, labels = TRUE)

## EXAMPLE 2 (Scrolling plot of PCA loadings)

data(cassav)
X <- cassav$Xtest
fm <- pcaeigenk(X, nlv = 20)
P <- fm$P

plotsp1(t(P), ylab = "Value")