DrawPCA: Draw the PCA scores or loadings of the signals

In PepsNMR: Pre-process 1H-NMR FID signals

Description

The function draws the PCA scores or loadings of the FIDs/spectra given in the matrix Signal_data.

Do not call this function directly but rather call Draw to specify how the plot will be returned.

Usage

DrawPCA(Signal_data, drawNames = TRUE,  main = "PCA score plot", Class = NULL, 
              axes = c(1,2), type.pca = c("scores", "loadings"), 
              loadingstype=c("l", "p"), num.stacked = 4, xlab = "rowname",
              createWindow)

Arguments

Signal_data	Matrix containing the FIDs or spectra, one line per FID/spectrum.
drawNames	If TRUE, the names of the spectra have to be shown alonside the points on the scores plot.
main	Plot title.
Class	Vector (numeric or character) indicating the class of each spectra. Used for scores plot only.
axes	Vector of score or loading numbers to be plotted. If it represents the score's numbers, only the first two elements are used.
type.pca	The type of plot, either "scores" or "loadings"
loadingstype	The type of loadings plot, either a line plot ("l") or points with histogram-like vertical lines ("p").
num.stacked	Number of stacked plots for the loadings plots.
xlab	Label of the x-axis of loadings plots.
createWindow	If TRUE, will open a new window to display the graphs.

Author(s)

Benoît Legat & Manon Martin

See Also

See also Draw and DrawSignal.

Examples

require(PepsNMRData)
# Draw loadings
DrawPCA(FinalSpectra_HS, main = "PCA loadings plot", 
      Class = NULL, axes =c(1,3, 5), type ="loadings", loadingstype="l", 
      num.stacked=4, xlab="ppm", createWindow = TRUE)

# Draw scores
class = substr(rownames(FinalSpectra_HS),5,5)
DrawPCA(FinalSpectra_HS, drawNames = TRUE, main = "PCA scores plot", 
        Class = class,  axes = c(1,2), type = "scores", createWindow = TRUE)

PepsNMR documentation built on Jan. 16, 2021, 2:07 a.m.