Package: ribiosPlot 1.3.0

Jitao David Zhang

ribiosPlot: Plotting Module of the 'ribios' Software Suite

Provides data structures and functions for data transformation and visualization in computational biology in drug discovery as part of the 'ribios' software suite. Zhang (2025) <https://github.com/bedapub/ribiosPlot>.

Authors:Jitao David Zhang [aut, cre, ctb]

ribiosPlot_1.3.0.tar.gz
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ribiosPlot_1.3.0.tgz(r-4.6-any)ribiosPlot_1.3.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
card.svg |card.png
ribiosPlot/json (API)
NEWS

# Install 'ribiosPlot' in R:
install.packages('ribiosPlot', repos = c('https://bedapub.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bedapub/ribiosplot/issues

On CRAN:

Conda:

4.86 score 1 stars 3 packages 32 scripts 145 downloads 84 exports 20 dependencies

Last updated from:7e00b2c76f. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK160
source / vignettesOK171
linux-release-x86_64OK147
macos-release-arm64OK133
macos-oldrel-arm64OK107
windows-develOK144
windows-releaseOK121
windows-oldrelOK178
wasm-releaseOK202

Exports:biosHeatmapblackgoldredblackgreenblackredblackredyellowblackwhiteblackyellowblueblackredblueredboundboundNormbrewer.pal.factorcascadeOrdercloseFileDevicecolorpanelcompactParcompactTrellisconfEllipsecyanblackyellowdegree2radiandisplay.colorpanelsdisplay.threecolor.panelsdisplay.twocolor.panelsellipseexpVarexpVarLabelfcbasefcbase<-fcbrewerfcolfigurePanelgetDefaultFontFamilygetExpVarLabelgetLimsgreenredguessWHheathistMatidevintRangeipdfjitter.xyplotmagentayellowmidColnonNullopenFileDevicep2asteriskpanel.corpanel.lmSmoothPCAScoreMatrixpcaScorespcaScoresFromLogFCpdf2pngplotPCAplotPCAloadingplotVennqBreaksqHistradian2degreeredblackblueredblueredgreenrobustDistrowVarsroyalbluegrayredroyalblueredroyalredblueroyalredgraybluesetCompactTrellissquareLayoutsymrangethreecolor.panelsturyebtwocolor.panelsvennMembersDataframevennMembersListwhiteblackwhitebluewhiteblueblackheatwhiteredxclipHistyellowblackyellowblackcyanyellowmagenta

Dependencies:clicpp11farverggplot2gluegridExtragtableisobandlabelinglatticelifecycleR6RColorBrewerribiosUtilsrlangS7scalesvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Subsetting PCAScoreMatrix while keeping the expVar attribute[.PCAScoreMatrix
Coerece a PCAScoreMatrix into data.frameas.data.frame.PCAScoreMatrix
Coerece a PCAScoreMatrix into score matrixas.matrix.PCAScoreMatrix
CUSTOMED HEATMAP.2 FOR BIOS USERSbiosHeatmap
Build brewer.pal colors from factor (Deprecated)brewer.pal.factor brewer.pal.factorLevels
Order rows of a matrix in the cascade ordercascadeOrder
Generates a set of colors that varies smoothly.colorpanel
Compact par settingcompactPar
Return a compact setting for lattice plots, useful for preparing publicationscompactTrellis
Plot confidence ellipse based on two-dimenstional dataconfEllipse
Convert degree to radian valuesdegree2radian
Display color panelsdisplay.colorpanels
Display three-color panelsdisplay.threecolor.panels
Display two-color panelsdisplay.twocolor.panels
Add an ellipse in an existing plotellipse
S3 function expVar to extract explained variance from prcomp and PCAScoreMatrix objectsexpVar expVar.PCAScoreMatrix expVar.prcomp
Generic function expVarLabel to generate a label of explained variance from prcomp and PCAScoreMatrix objectsexpVarLabel
Labels of principal components from PCAScoreMatrixexpVarLabel.PCAScoreMatrix
Labels of principal components from prcompexpVarLabel.prcomp
Return base colors of a fcol objectfcbase
Replace base colors of a fcol object with a different valuefcbase<-
Factor color brewerfcbrewer
Construct a fcol objectfcol
Make a figure panel with titlefigurePanel
Get default font familygetDefaultFontFamily
Helper function to print PC and explained variancesgetExpVarLabel
Get xlim/ylim ranges for plots from real valuesgetLims
Mimicking the graphics::smoothScatter behaviour for GGally::ggpairsggSmoothScatter
Mimicking the graphics::smoothScatter behaviour for GGally::ggpairs, with aux linesggSmoothScatterWithAux
Guess width and height parameters for a heatmapguessWH
Make histograms for matrixhistMat
Interative dev.print and pdf printidev ipdf
Return a range defined by integersintRange
Make boxplots or dotplots with sample-size proportional jittersjitter.xyplot
Blender two colors to get the midpoint color of two colorsmidCol
Make sure that x is assigned a reasonable valuenonNull
Open a device as a file preparing for plotting in the filecloseFileDevice openFileDevice
Convert p values into asterisksp2asterisk
Correlation panel for pairspanel.cor
Correlation panelpanel.lmSmooth
Retrieve PCA rotations from prcomp objectspcaRotation
Construct a S3-class PCAScoreMatrix objectPCAScoreMatrix
Retrieve PCA scores from prcomp objectspcaScores
Perform principal component analysis and derive PCA scores from a logFC matrixpcaScoresFromLogFC
Use 'convert' (ImageMagick) to convert PDF to high-quality PNGpdf2png
S3 method plotPCAplotPCA
Visualise PCA results of expression data with the sample plotplotPCA.prcomp
Plot PCA loadingplotPCAloading
Plot Venn object of the Vennerable packageplotVenn
Print a fcol objectprint.fcol
Print PCAScoreMatrixprint.PCAScoreMatrix
Internal function to re-calculate breaks of histograms when x-axis is clippedqBreaks
Histogram with quantile line(s) and text(s)qHist
Convert radian to degree valuesradian2degree
Robust distancerobustDist
Two and three-color panelsblackgoldred blackgreen blackred blackredyellow blackwhite blackyellow blueblackred bluered cyanblackyellow greenred heat magentayellow redblackblue redblue redgreen royalbluegrayred royalbluered royalredblue royalredgrayblue turyeb whiteblack whiteblue whiteblueblackheat whitered yellowblack yellowblackcyan yellowmagenta
Set compact trellis as defaultsetCompactTrellis
Plan a square/matrix layout of plotssquareLayout
Return a symmetric rangesymrange
Return available three-color panelsthreecolor.panels
Return available three-color panelstwocolor.panels
Extract members of each region in Venn diagrams in to a data.framevennMembersDataframe
Extract members of each region in Venn diagrams in to a listvennMembersList
Histogram with clipped x axisxclipHist