An R package for performing Principal Component Analysis-based Data Structure Comparisons (PCADSC)
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README.md

PCADSC

Development version of the R package PCADSC. The last stable version of the package can be installed from CRAN using:

install.packages('PCADSC')

To install the development version of PCADSC, run the following commands from within R:

library(devtools)
install_github('annepetersen1/PCADSC')

The PCADSC methods are described in our article manuscript.

The basic functionality of the package can be inspected using the following lines of code:

library(PCADSC)

#Load iris data
data(iris)

#Define grouping variable, grouping the observations by whether their species is
#Setosa or not
iris$group <- "setosa"
iris$group[iris$Species != "setosa"] <- "non-setosa"

#Make a PCADSC object, splitting the data by "group"
irisPCADSC <-PCADSC(iris, "group", var=setdiff(names(iris), c("group", "Species")),
                    doCE = TRUE, doAngle = TRUE, doChroma = TRUE)
                         
#Make a cumulative eigenvalue (CE) plot
CEPlot(irisPCADSC)

#Make an angle plot 
anglePlot(irisPCADSC)

#Make a chroma plot
chromaPlot(irisPCADSC)

Our current to-do list for the package is posted below. If you have any further suggestions for added functionality, or have a bug to report, please open an issue and let us know.

To do

  • Make print() methods for pcaRes, CEInfo, angleInfo, chromaInfo and PCASDC objects
  • Make summary() methods for pcaRes, CEInfo, angleInfo, chromaInfo and PCASDC object