Package: RPointCloud 0.8.0
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:
RPointCloud_0.8.0.tar.gz
RPointCloud_0.8.0.tar.gz(r-4.5-noble)RPointCloud_0.8.0.tar.gz(r-4.4-noble)
RPointCloud_0.8.0.tgz(r-4.4-emscripten)RPointCloud_0.8.0.tgz(r-4.3-emscripten)
RPointCloud.pdf |RPointCloud.html✨
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
- 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
Last updated 3 months agofrom:6e87da9d13. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 01 2024 |
| R-4.5-linux | OK | Dec 01 2024 |
Exports:angleMeanscutoffcutoffSignificantCyclecycleSupportdisentangleEBexpoExpoFitFeaturegetCyclehistimageLDPClinesLoopCircosLoopFeatureplotpointsProjectiontailHistotakensvoidFeaturevoidPlot
Dependencies:ade4askpassbase64encBHBiobaseBiocGenericsbslibcachemchangepointcirclizeClassComparisonClassDiscoverycliclueclustercolorspacecpmcpp11dendextenddigestevaluatefansifarverfastmapflexmixFNNfontawesomefsgenericsggplot2GlobalOptionsgluegridExtragtableherehighrhtmltoolshtmlwidgetsigraphisobandjquerylibjsonlitekernlabKernSmoothknitrkohonenlabelinglatticelifecyclemagrittrMASSMatrixmclustmemoiseMercatormgcvmimemodeltoolsmovMFmunsellnlmennetoompaBaseoompaDataopensslPCDimensionpillarpixmappkgconfigpngPolychromeR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLreticulaterglrlangrmarkdownrprojrootRSpectraRtsnesassscalesscatterplot3dshapeskmeansslamspsysTDAThreshertibbletinytexumaputf8vctrsviridisviridisLitewithrxfunyamlzoo
RPointCloud: A Mass Cytometry Example
Rendered fromcytof.Rmdusingknitr::rmarkdownon Dec 01 2024.Last update: 2024-06-26
Started: 2024-06-26
RPointCloud: CLL Clinical Data
Rendered fromclinical.Rmdusingknitr::rmarkdownon Dec 01 2024.Last update: 2024-08-20
Started: 2024-06-26
RPointCloud: Regulatory T Cells
Rendered fromtreg.Rmdusingknitr::rmarkdownon Dec 01 2024.Last update: 2024-06-26
Started: 2024-06-26
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Chronic Lymphocytic Leukemia Clinical Data | clinical CLL-data daisydist ripdiag |
| 'Cycle' Objects For Visualizing Topological Data Analysis Results | Cycle Cycle-class cycleSupport getCycle lines,Cycle-method plot,Cycle,matrix-method |
| CyTOF Data | AML10.node287 AML10.node287.rips Arip cytof-data |
| Disentangling Rips Diagrams From Their Initial Data Coordinates | disentangle |
| The 'EBexpo' Class | cutoff EBexpo EBexpo-class hist,EBexpo-method plot,EBexpo,missing-method |
| The 'ExpoFit' Class | ExpoFit ExpoFit-class plot,ExpoFit,missing-method |
| 'Feature' Objects For Visualizing Topological Data Anal;ysis Results | Feature Feature-class plot,Feature,matrix-method points,Feature-method |
| Local Dimension of Point Clouds | LDPC takens |
| The 'LoopCircos' Class | angleMeans image,LoopCircos-method LoopCircos LoopCircos-class |
| 'LoopFeature' Objects For Visualizing Features That Define Loops | image,LoopFeature-method LoopFeature LoopFeature-class plot,LoopFeature,character-method plot,LoopFeature,missing-method |
| 'Projection' Objects For Visualizing 3D Topological Data Analysis Results in 2D | image,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) Cells | rip tmat treg treg-data |
| 3D Scatter Plots of Cycles and Features | voidFeature voidPlot voids |