R: Plotting Module of the 'ribios' Software Suite

# Plotting Module of the 'ribios' Software Suite

## Documentation for package ‘ribiosPlot’ version 1.3.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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
blackgoldred | Two and three-color panels
blackgreen | Two and three-color panels
blackred | Two and three-color panels
blackredyellow | Two and three-color panels
blackwhite | Two and three-color panels
blackyellow | Two and three-color panels
blueblackred | Two and three-color panels
bluered | Two and three-color panels
brewer.pal.factor | Build brewer.pal colors from factor (Deprecated)
brewer.pal.factorLevels | Build brewer.pal colors from factor (Deprecated)
cascadeOrder | Order rows of a matrix in the cascade order
closeFileDevice | Open a device as a file preparing for plotting in the file
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
cyanblackyellow | Two and three-color panels
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
expVar.PCAScoreMatrix | S3 function expVar to extract explained variance from prcomp and PCAScoreMatrix objects
expVar.prcomp | 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
greenred | Two and three-color panels
guessWH | Guess width and height parameters for a heatmap
heat | Two and three-color panels
histMat | Make histograms for matrix
idev | Interative dev.print and pdf print
intRange | Return a range defined by integers
ipdf | Interative dev.print and pdf print
jitter.xyplot | Make boxplots or dotplots with sample-size proportional jitters
magentayellow | Two and three-color panels
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
PCAScoreMatrix | Construct a S3-class PCAScoreMatrix object
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.fcol | Print a fcol object
print.PCAScoreMatrix | Print PCAScoreMatrix
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
redblackblue | Two and three-color panels
redblue | Two and three-color panels
redgreen | Two and three-color panels
robustDist | Robust distance
royalbluegrayred | Two and three-color panels
royalbluered | Two and three-color panels
royalredblue | Two and three-color panels
royalredgrayblue | 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
turyeb | Two and 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
whiteblack | Two and three-color panels
whiteblue | Two and three-color panels
whiteblueblackheat | Two and three-color panels
whitered | Two and three-color panels
xclipHist | Histogram with clipped x axis
yellowblack | Two and three-color panels
yellowblackcyan | Two and three-color panels
yellowmagenta | Two and three-color panels
[.PCAScoreMatrix | Subsetting PCAScoreMatrix while keeping the expVar attribute