Package: Radviz 0.9.5

Radviz: Project Multidimensional Data in 2D Space

An implementation of the radviz projection in R. It enables the visualization of multidimensional data while maintaining the relation to the original dimensions. This package provides functions to create and plot radviz projections, and a number of summary plots that enable comparison and analysis. For reference see Hoffman *et al.* (1999) (<doi:10.1145/331770.331775>) for original implementation, see Di Caro *et al* (2012) (<doi:10.1007/978-3-642-13672-6_13>), for the original method for dimensional anchor arrangements, see Demsar *et al.* (2007) (<doi:10.1016/j.jbi.2007.03.010>) for the original Freeviz implementation.

Authors:Yann Abraham [aut, cre], Nicolas Sauwen [aut]

Radviz_0.9.5.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Radviz/json (API)

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

Bug tracker:https://github.com/yannabraham/radviz/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

high-dimensional-dataradvizsciencevisualizationcpp

6.60 score 11 stars 60 scripts 334 downloads 3 mentions 25 exports 32 dependencies

Last updated from:b148719b8e. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK170
linux-devel-x86_64OK163
source / vignettesOK380
linux-release-arm64OK153
linux-release-x86_64OK163
macos-release-arm64OK157
macos-release-x86_64OK347
macos-oldrel-arm64OK96
macos-oldrel-x86_64OK210
windows-develOK155
windows-releaseOK173
windows-oldrelOK135
wasm-releaseOK127

Exports:anchor.filterbubbleRadvizcosineDB_weightedIdxdo.densitydo.hexdo.Ldo.optimdo.optimFreevizdo.optimGraphvizdo.optimRadvizdo.radvizget.optimhexplotin.dais.radvizis.validmake.SrecenterrescalePlotrv.dasmoothRadvizspringstheme_radviztuneForceRatio

Dependencies:clicpp11dplyrfarvergenericsggplot2gluegtablehexbinigraphisobandlabelinglatticelifecyclemagrittrMatrixpillarpkgconfigpracmaR6RColorBrewerRcppRcppArmadillorlangS7scalestibbletidyselectutf8vctrsviridisLitewithr

Multivariate Functional analysis
Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators | Data acquisition and preparation | Effects of stimulation on B and T cells | Collecting single cell data | CD8^+^ T and IgM^+^ B cells profile | Phenotypic | Functional | Selecting channels relevant to T cells | Using Radviz to visualize the effects of stimulation | Using Freeviz to visualize the effects of stimulation | Building a functional T cells graph | Building a cell-level distance matrix | Extracting an adjacency matrix | Computing edge weights from adjacency matrix | Building a kNN graph | Extracting communities as functional states | From communities to functional states | Using Graphviz to visualize functional graph
Rendered frommultivariate_analysis.Rmdusingknitr::rmarkdown

Last update: 2025-05-08
Started: 2020-03-16

Visualizing Multivariate Data with Radviz
Abstract | Introduction | Building a Radviz projection | Installation | Visualizing High Dimensional Data: the bodenmiller dataset | Normalizing the data | Defining the anchors | Optimizing the position of anchors | Projection | Visualizing the results | Visualizing Signal Intensity for Functional Channels | Visualizing Cell Populations | Visualizing Functional Changes
Rendered fromsingle_cell_projections.Rmdusingknitr::rmarkdown

Last update: 2025-05-08
Started: 2016-02-24

Readme and manuals

Help Manual

Help pageTopics
Filtering out anchors with low contributions to the projectionanchor.filter
A Plotting Function for the Radviz ObjectbubbleRadviz
Plots the Dimensional Anchors and density lines for projected data points in a 2D space.contour.radviz
Compute the Cosine Similarity between the Columns of a Data Setcosine
Computation of weighted version of the Davies-Bouldin index. This index serves as a measure of clustering quality of a 2D projection result with known class labelsDB_weightedIdx
Perform L-Normalization on a Vectordo.L
Optimize the Dimensional Anchors Position using the Freeviz algorithmdo.optimFreeviz
Optimize the Dimensional Anchors Position using the Graphviz algorithmdo.optimGraphviz
Optimize the Dimensional Anchors Position for Radviz projection using a Genetic Algorithmdo.optim do.optimRadviz
Projects a Matrix or a Data Frame to a 2D space defined by Dimensional Anchorsdo.radviz do.radviz.default
Get the Result of the Optimization Operationget.optim
A hexplot function for Radviz objectshexplot
Optimization functions for Dimensional Anchors in Radvizin.da rv.da
Test if the object is a Radviz objectis.radviz
Identify the valid projections from a Radviz objectis.valid
Define Dimensional Anchors around the Unit Circlemake.S
A Plotting Function for the Radviz Objectplot.radviz
Rotate Dimensional Anchors around the Unit Circlerecenter
Rescaling of projected data for plottingrescalePlot
A smoothScatter function for Radviz objectssmoothRadviz
Subsetting a Radviz projectionsubset.radviz
Radviz Object Summary, head, print, dim and springs Methodsdim.radviz head.radviz print.radviz springs summary.radviz
Text annotations for for the Radviz Plotstext.radviz
Complete ggplot2 theme for Radviz projectionstheme_radviz
Method to compute optimal ratio between repulsive and attractive forces for Freeviz.tuneForceRatio