PcaPlots: PCA plots
In NormalizeMets: Analysis of Metabolomics Data

Description Usage Arguments Author(s) See Also Examples

Produces PCA plots of the metabolomics data.

PcaPlots(featuredata, groupdata, saveplot = FALSE,
  saveinteractiveplot = FALSE, plotname = "", savetype = c("png", "bmp",
  "jpeg", "tiff", "pdf"), interactiveonly = FALSE, interactiveplots = TRUE,
  y.axis = 1, x.axis = 2, center = TRUE, scale = TRUE,
  userinput = TRUE, returninteractive = FALSE, main = NULL,
  varplot = FALSE, multiplot = FALSE, n = 3, cols = NULL,
  cex_val = 0.7, ...)

`featuredata`	featuredata A data frame in the featuredata format. This is a dataframe with metabolites in columns and samples in rows. Unique sample names should be provided as row names. See NormalizeMets Vignette for details.
`groupdata`	A data frame or a vector with group names.
`saveplot`	A logical indication whether to save the plot produced.
`saveinteractiveplot`	A logical indication whether to save the interactive plots produced.
`plotname`	Name of the output file if the file is to be saved. This is the general name for all the graphs and the specific type prefix will be added automatically.
`savetype`	The required format for the plot to be saved in. Threre is a choice of `"png","bmp","jpeg","tiff","pdf"` type files.
`interactiveonly`	Alogical indicating whether to show interactive plots only.
`interactiveplots`	A logical indication whether an interactive plot is to be shown.
`y.axis`	The principal component to be plotted on the y-axis.
`x.axis`	The principal component to be plotted on the x-axis.
`center`	A logical indicating whether the variables should be scaled to have zero mean.
`scale`	A logical indicating whether the variables should be scaled to have unit variance before the analysis takes place.
`userinput`	A logical indication whether user input should be required to show plots progressively. Should be `FALSE` when the plots are to be passed on to other functions or saved as variables for later use.
`returninteractive`	A logical indication whether a list of the interactive plots should be returned by the function
`main`	Plot title.
`varplot`	A logical indicating whether explained variance should be plotted.
`multiplot`	If `TRUE`, pairs plots of the first n principal components will be plotted.
`n`	The number of principal components to be plotted if `multiplot=TRUE`. The default value is set to 5.
`cols`	A character string with colours to be used.
`cex_val`	A numeric indicating the size of some text elements.
`...`	Arguments to be passed on to other methods.

Alysha M De Livera, Gavriel Olshansky

prcomp.

    data(mixdata)
    
    # produce all results
    PcaPlots(mixdata$featuredata,mixdata$sampledata[,3],multiplot = TRUE, 
    varplot = TRUE, interactiveplots = TRUE)
    
    # return a list of the ineractive plots only
    interactive.pca <- PcaPlots(mixdata$featuredata,mixdata$sampledata[,3],
    interativeonly = TRUE, interactiveplots = TRUE,
    userinput = FALSE, returninteractive = TRUE)