Package: RPointCloud 0.9.1

Kevin R. Coombes

RPointCloud: Visualizing Topological Loops and Voids

Visualizations to explain the results of a topological data analysis. The goal of topological data analysis is to identify persistent topological structures, such as loops (topological circles) and voids (topological spheres), in data sets. The output of an analysis using the 'TDA' package is a Rips diagram (named after the mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in these holes in the data by providing tools to visualize the features that help explain the structures found in the Rips diagram. See McGee and colleagues (2024) <doi:10.1101/2024.05.16.593927>.

Authors:Kevin R. Coombes [aut, cre], Jake Reed [aut], RB McGee [aut]

RPointCloud_0.9.1.tar.gz
RPointCloud_0.9.1.tar.gz(r-4.7-any)RPointCloud_0.9.1.tar.gz(r-4.6-any)
RPointCloud_0.9.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
RPointCloud/json (API)

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

Bug tracker:https://r-forge.r-project.org/projects/oompa

Datasets:
  • AML10.node287 - CyTOF Data
  • AML10.node287.rips - CyTOF Data
  • Arip - CyTOF Data
  • clinical - Chronic Lymphocytic Leukemia Clinical Data
  • daisydist - Chronic Lymphocytic Leukemia Clinical Data
  • rip - Single Cell Data on T Regulatory (Treg) Cells
  • ripdiag - Chronic Lymphocytic Leukemia Clinical Data
  • tmat - Single Cell Data on T Regulatory (Treg) Cells
  • treg - Single Cell Data on T Regulatory (Treg) Cells

On CRAN:

Conda:

2.92 score 28 scripts 183 downloads 23 exports 100 dependencies

Last updated from:31f352887a. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK219
source / vignettesOK351
linux-release-x86_64OK229
wasm-releaseOK186

Exports:angleMeanscutoffcutoffSignificantCyclecycleSupportdisentangleEBexpoExpoFitFeaturegetCyclehistimageLDPClinesLoopCircosLoopFeatureplotpointsProjectiontailHistotakensvoidFeaturevoidPlot

Dependencies:ade4askpassbase64encBHBiobaseBiocGenericsbslibcachemchangepointcirclizeClassComparisonClassDiscoverycliclueclustercolorspacecpmcpp11dendextenddigestevaluatefarverfastmapflexmixFNNfontawesomefsgenericsggplot2GlobalOptionsgluegridExtragtableherehighrhtmltoolshtmlwidgetsigraphisobandjquerylibjsonlitekernlabKernSmoothknitrkohonenlabelinglatticelifecyclemagrittrMASSMatrixmclustmemoiseMercatormimemodeltoolsmovMFnnetoompaBaseoompaDataopensslPCDimensionpixmappkgconfigpngPolychromeR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLreticulaterglrlangrmarkdownrprojrootRSpectraRtsneS7sassscalesscatterplot3dshapeskmeansslamspsysTDAThreshertinytexumapvctrsviridisviridisLitewithrxfunyamlzoo

RPointCloud: A Mass Cytometry Example
Introduction | TDA Built-in Visualizations of the Rips Diagram | Mercator Visualizations of the Underlying Data and Distance Matrix | Dimension Zero | Using iGraph | Community Structure | Visualizing Features | Significance | Zero-Cycles (Connected Components) | One-Cycles (Loops) | Two-Cycles (Voids)
Rendered fromcytof.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2024-06-26

RPointCloud: CLL Clinical Data
Introduction | TDA Built-in Visualizations of the Rips Diagram | Mercator Visualizations of the Underlying Data and Distance Matrix | Dimension Zero | Using iGraph | Community Structure | Visualizing Features | Significance | Zero-Cycles (Connected Components) | One-Cycles (Loops) | Two-Cycles (Voids)
Rendered fromclinical.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2024-06-26

RPointCloud: Regulatory T Cells
Introduction | TDA Built-in Visualizations of the Rips Diagram | Mercator Visualizations of the Underlying Data and Distance Matrix | Dimension Zero | Using iGraph | Community Structure | Visualizing Features
Rendered fromtreg.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2024-06-26

Readme and manuals

Help Manual

Help pageTopics
Chronic Lymphocytic Leukemia Clinical Dataclinical CLL-data daisydist ripdiag
'Cycle' Objects For Visualizing Topological Data Analysis ResultsCycle Cycle-class cycleSupport getCycle lines,Cycle-method plot,Cycle,matrix-method
CyTOF DataAML10.node287 AML10.node287.rips Arip cytof-data
Disentangling Rips Diagrams From Their Initial Data Coordinatesdisentangle
The 'EBexpo' Classcutoff EBexpo EBexpo-class hist,EBexpo-method plot,EBexpo,missing-method
The 'ExpoFit' ClassExpoFit ExpoFit-class plot,ExpoFit,missing-method
'Feature' Objects For Visualizing Topological Data Anal;ysis ResultsFeature Feature-class plot,Feature,matrix-method points,Feature-method
Local Dimension of Point CloudsLDPC takens
The 'LoopCircos' ClassangleMeans image,LoopCircos-method LoopCircos LoopCircos-class
'LoopFeature' Objects For Visualizing Features That Define Loopsimage,LoopFeature-method LoopFeature LoopFeature-class plot,LoopFeature,character-method plot,LoopFeature,missing-method
'Projection' Objects For Visualizing 3D Topological Data Analysis Results in 2Dimage,Projection-method plot,Projection,missing-method Projection Projection-class
Function to extract the right tail of a histogram for display purposes.tailHisto
Single Cell Data on T Regulatory (Treg) Cellsrip tmat treg treg-data
3D Scatter Plots of Cycles and FeaturesvoidFeature voidPlot voids