| runPCA {EMA} | R Documentation |
This function performs a Principal Component Analysis (PCA) and represents the samples or the variables of the analysis.
runPCA(X, ncp=5, scale=TRUE, ind.sup=NULL, quanti.sup=NULL,quali.sup=NULL, sample.qual=TRUE, variable.qual=FALSE, sample.cont=TRUE,variable.cont=FALSE, plotSample=TRUE, plotVariable=FALSE, plotInertia = TRUE,plotBiplot=FALSE, plot3dSample=FALSE, lab.sample="quality", lab.var=NULL,palette="rainbow", lim.cos2.sample=0, lim.cos2.var=0, pdf=FALSE, pdfname= NULL, verbose=FALSE, ...)
X |
a data frame with n rows (samples) and p columns (variables) |
ncp |
number of dimensions kept in the results (by default 5) |
scale |
a boolean, if TRUE (value set by default) then data are scaled to unit variance |
ind.sup |
a vector indicating the indexes of the supplementary individuals |
quanti.sup |
a vector indicating the indexes of the quantitative supplementary variables |
quali.sup |
a vector indicating the indexes of the qualitative supplementary variables |
sample.qual |
a boolean, if TRUE quality sample is displayed, by default = TRUE |
variable.qual |
a boolean, if TRUE quality variable is displayed, by default = FALSE |
sample.cont |
a boolean, if TRUE sample contribution is displayed, by default = TRUE |
variable.cont |
a boolean, if TRUE variable contribution is displayed, by default = FALSE |
plotSample |
a boolean, if TRUE samples are displayed, by default = TRUE |
plotVariable |
a boolean, if TRUE variables are displayed, by default = FALSE |
plotInertia |
a boolean, if TRUE inertia percentage of components is displayed, by default = TRUE |
plotBiplot |
a boolean, if TRUE biplot is displayed, by default = FALSE |
plot3dSample |
a boolean, if TRUE sample 3D plot is displayed, by default = FALSE |
lab.sample |
a vector, sample representation is colored by label.sample, by default = NULL |
lab.var |
a vector, variable representation is colored by label.var, by default = "quality" |
palette |
character, name of palette color, by default = "rainbow" |
lim.cos2.sample |
a numeric, for graphics, keep samples with cos2 >= lim.cos2.sample, by default = 0 |
lim.cos2.var |
a numeric, for graphics, keep variables with cos2 >= lim.cos2.var, by default = 0 |
pdf |
a boolean, if TRUE save all the graphics in a pdf file, by default = FALSE |
pdfname |
pdf file name for saving graphics |
verbose |
print results if verbose = TRUE, by default = FALSE |
... |
Arguments to be passed to methods, such as graphical parameters (see 'par'). |
eig |
a matrix containing all the eigenvalues, the percentage of variance and the cumulative percentage of variance |
var |
a list of matrices containing all the results for the active variables (coordinates, correlation between variables and axes, square cosine, contributions |
ind |
a list of matrices containing all the results for the active individuals (coordinates, square cosine, contributions) |
Returns the individuals factor map for axes 1 and 2, 1 and 3, 2 and 3 Returns the inertia percentage of components By default, print sample coordinates, sample quality and sample contribution
EMA group
plotSample, plotVariable, plotInertia
data("marty")
## PCA on sample with inertia plot and sample plot colored by tumour type
example.subset <- marty[1:100,]
pca <- runPCA(t(example.subset), verbose = FALSE, lab.sample = marty.type.cl)