PCAScoreMatrix          Construct a S3-class PCAScoreMatrix object
[.PCAScoreMatrix        Subsetting PCAScoreMatrix while keeping the
                        expVar attribute
as.data.frame.PCAScoreMatrix
                        Coerece a PCAScoreMatrix into data.frame
as.matrix.PCAScoreMatrix
                        Coerece a PCAScoreMatrix into score matrix
biosHeatmap             CUSTOMED HEATMAP.2 FOR BIOS USERS
brewer.pal.factor       Build brewer.pal colors from factor
                        (Deprecated)
cascadeOrder            Order rows of a matrix in the cascade order
colorpanel              Generates a set of colors that varies smoothly.
compactPar              Compact par setting
compactTrellis          Return a compact setting for lattice plots,
                        useful for preparing publications
confEllipse             Plot confidence ellipse based on
                        two-dimenstional data
degree2radian           Convert degree to radian values
display.colorpanels     Display color panels
display.threecolor.panels
                        Display three-color panels
display.twocolor.panels
                        Display two-color panels
ellipse                 Add an ellipse in an existing plot
expVar                  S3 function expVar to extract explained
                        variance from prcomp and PCAScoreMatrix objects
expVarLabel             Generic function expVarLabel to generate a
                        label of explained variance from prcomp and
                        PCAScoreMatrix objects
expVarLabel.PCAScoreMatrix
                        Labels of principal components from
                        PCAScoreMatrix
expVarLabel.prcomp      Labels of principal components from prcomp
fcbase                  Return base colors of a fcol object
fcbase<-                Replace base colors of a fcol object with a
                        different value
fcbrewer                Factor color brewer
fcol                    Construct a fcol object
figurePanel             Make a figure panel with title
getDefaultFontFamily    Get default font family
getExpVarLabel          Helper function to print PC and explained
                        variances
getLims                 Get xlim/ylim ranges for plots from real values
ggSmoothScatter         Mimicking the graphics::smoothScatter behaviour
                        for GGally::ggpairs
ggSmoothScatterWithAux
                        Mimicking the graphics::smoothScatter behaviour
                        for GGally::ggpairs, with aux lines
guessWH                 Guess width and height parameters for a heatmap
histMat                 Make histograms for matrix
idev                    Interative dev.print and pdf print
intRange                Return a range defined by integers
jitter.xyplot           Make boxplots or dotplots with sample-size
                        proportional jitters
midCol                  Blender two colors to get the midpoint color of
                        two colors
nonNull                 Make sure that x is assigned a reasonable value
openFileDevice          Open a device as a file preparing for plotting
                        in the file
p2asterisk              Convert p values into asterisks
panel.cor               Correlation panel for pairs
panel.lmSmooth          Correlation panel
pcaRotation             Retrieve PCA rotations from prcomp objects
pcaScores               Retrieve PCA scores from prcomp objects
pcaScoresFromLogFC      Perform principal component analysis and derive
                        PCA scores from a logFC matrix
pdf2png                 Use 'convert' (ImageMagick) to convert PDF to
                        high-quality PNG
plotPCA                 S3 method plotPCA
plotPCA.prcomp          Visualise PCA results of expression data with
                        the sample plot
plotPCAloading          Plot PCA loading
plotVenn                Plot Venn object of the Vennerable package
print.PCAScoreMatrix    Print PCAScoreMatrix
print.fcol              Print a fcol object
qBreaks                 Internal function to re-calculate breaks of
                        histograms when x-axis is clipped
qHist                   Histogram with quantile line(s) and text(s)
radian2degree           Convert radian to degree values
robustDist              Robust distance
royalbluered            Two and three-color panels
setCompactTrellis       Set compact trellis as default
squareLayout            Plan a square/matrix layout of plots
symrange                Return a symmetric range
threecolor.panels       Return available three-color panels
twocolor.panels         Return available three-color panels
vennMembersDataframe    Extract members of each region in Venn diagrams
                        in to a data.frame
vennMembersList         Extract members of each region in Venn diagrams
                        in to a list
xclipHist               Histogram with clipped x axis
