Learn R Programming

ribiosPlot: Data transformation and visualisation

What is ribiosPlot?

ribiosPlot is a R package in the ribios suite that assists data transformation and visualization.

Installation

ribiosPlot depends on the ribiosUtils package, which should be installed first.

Run following commands in the R console.

library(devtools)
devtools::install_github("bedapub/ribiosPlot")

Todo

  1. NAMESPACE and Rd files are not generated by roxygen2.
  2. make check is not clean yet.

Copy Link

Version

Install

install.packages('ribiosPlot')

Version

1.3.0

License

GPL-3

Issues

0

Pull Requests

0

Stars

1

Forks

1

Maintainer

Jitao David Zhang

Last Published

February 25th, 2026

Functions in ribiosPlot (1.3.0)

expVarLabel.PCAScoreMatrix

Labels of principal components from PCAScoreMatrix
expVarLabel

Generic function expVarLabel to generate a label of explained variance from prcomp and PCAScoreMatrix objects
guessWH

Guess width and height parameters for a heatmap
fcbrewer

Factor color brewer
figurePanel

Make a figure panel with title
fcbase

Return base colors of a fcol object
ggSmoothScatterWithAux

Mimicking the graphics::smoothScatter behaviour for GGally::ggpairs, with aux lines
fcol

Construct a fcol object
fcbase<-

Replace base colors of a fcol object with a different value
getDefaultFontFamily

Get default font family
expVarLabel.prcomp

Labels of principal components from prcomp
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
intRange

Return a range defined by integers
nonNull

Make sure that x is assigned a reasonable value
jitter.xyplot

Make boxplots or dotplots with sample-size proportional jitters
p2asterisk

Convert p values into asterisks
panel.cor

Correlation panel for pairs
nonNegCascadeOrder

Order rows of a matrix with non-negative maximum values in the cascade order
openFileDevice

Open a device as a file preparing for plotting in the file
midCol

Blender two colors to get the midpoint color of two colors
idev

Interative dev.print and pdf print
histMat

Make histograms for matrix
panel.lmSmooth

Correlation panel
plotPCAloading

Plot PCA loading
plotPCA.prcomp

Visualise PCA results of expression data with the sample plot
plotPCA

S3 method plotPCA
pcaScores

Retrieve PCA scores from prcomp objects
pdf2png

Use 'convert' (ImageMagick) to convert PDF to high-quality PNG
pcaScoresFromLogFC

Perform principal component analysis and derive PCA scores from a logFC matrix
pcaRotation

Retrieve PCA rotations from prcomp objects
plotVenn

Plot Venn object of the Vennerable package
print.PCAScoreMatrix

Print PCAScoreMatrix
qHist

Histogram with quantile line(s) and text(s)
print.fcol

Print a fcol object
ribiosPlot-package

ribiosPlot: Plotting Module of the 'ribios' Software Suite
reexports

Objects exported from other packages
royalbluered

Two and three-color panels
radian2degree

Convert radian to degree values
setCompactTrellis

Set compact trellis as default
robustDist

Robust distance
rowVars

Variance of features in rows
symrange

Return a symmetric range
squareLayout

Plan a square/matrix layout of plots
qBreaks

Internal function to re-calculate breaks of histograms when x-axis is clipped
[.PCAScoreMatrix

Subsetting PCAScoreMatrix while keeping the expVar attribute
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
xclipHist

Histogram with clipped x axis
vennMembersList

Extract members of each region in Venn diagrams in to a list
compactPar

Compact par setting
as.matrix.PCAScoreMatrix

Coerece a PCAScoreMatrix into score matrix
PCAScoreMatrix

Construct a S3-class PCAScoreMatrix object
as.data.frame.PCAScoreMatrix

Coerece a PCAScoreMatrix into data.frame
colorpanel

Generates a set of colors that varies smoothly.
confEllipse

Plot confidence ellipse based on two-dimenstional data
brewer.pal.factor

Build brewer.pal colors from factor (Deprecated)
biosHeatmap

CUSTOMED HEATMAP.2 FOR BIOS USERS
compactTrellis

Return a compact setting for lattice plots, useful for preparing publications
cascadeOrder

Order rows of a matrix in the cascade order
ellipse

Add an ellipse in an existing plot
expVar

S3 function expVar to extract explained variance from prcomp and PCAScoreMatrix objects
display.threecolor.panels

Display three-color panels
display.colorpanels

Display color panels
degree2radian

Convert degree to radian values
display.twocolor.panels

Display two-color panels