{ "_id": "6a1efe74b401979e73419d9f", "Package": "RPointCloud", "Version": "0.9.1", "Date": "2026-02-17", "Title": "Visualizing Topological Loops and Voids", "Authors@R": "c(person(\"Kevin R.\", \"Coombes\", role = c(\"aut\", \"cre\"),\nemail = \"krc@silicovore.com\"),\nperson(\"Jake\", \"Reed\", role = c(\"aut\"),\nemail = \"reed01@augusta.edu\"),\nperson(\"RB\", \"McGee\", role = c(\"aut\"),\nemail = \"mcgee@haverford.edu\"))", "Description": "Visualizations to explain the results of a topological\ndata analysis. The goal of topological data analysis is to\nidentify persistent topological structures, such as loops\n(topological circles) and voids (topological spheres), in data\nsets. The output of an analysis using the 'TDA' package is a\nRips diagram (named after the mathematician Eliyahu Rips). The\ngoal of 'RPointCloud' is to fill in these holes in the data by\nproviding tools to visualize the features that help explain the\nstructures found in the Rips diagram. See McGee and colleagues\n(2024) .", "License": "Artistic-2.0", "URL": "http://oompa.r-forge.r-project.org/", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-18 09:29:42 UTC", "User": "root" }, "Author": "Kevin R. Coombes [aut, cre], Jake Reed [aut], RB McGee [aut]", "Maintainer": "Kevin R. Coombes ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-02-17 21:10:08 UTC", "RemoteUrl": "https://github.com/cran/RPointCloud", "RemoteRef": "HEAD", "RemoteSha": "31f352887abc633c0cc765d29df9a700618ce072", "MD5sum": "e486e299497400f10a3ea937b010b416", "_user": "cran", "_type": "src", "_file": "RPointCloud_0.9.1.tar.gz", "_fileid": "ae4ecd67560b33b73b81350f11951b09b5cadf6462c0876ff4321cbc734cde96", "_filesize": 9787745, "_sha256": "ae4ecd67560b33b73b81350f11951b09b5cadf6462c0876ff4321cbc734cde96", "_created": "2026-05-18T09:29:42.000Z", "_published": "2026-06-02T16:01:56.555Z", "_distro": "noble", "_jobs": [ { "job": 79114725611, "time": 206, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7054259178" }, { "job": 79114725783, "time": 232, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7054268117" }, { "job": 79114725320, "time": 388, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7054183505" }, { "job": 79114724879, "time": 195, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7363087659" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26024827956", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/RPointCloud", "_commit": { "id": "31f352887abc633c0cc765d29df9a700618ce072", "author": "Kevin R. Coombes ", "committer": "cran-robot ", "message": "version 0.9.1\n", "time": 1771362608 }, "_maintainer": { "name": "Kevin R. Coombes", "email": "krc@silicovore.com" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "TDA", "role": "Imports" }, { "package": "ClassDiscovery", "role": "Imports" }, { "package": "ClassComparison", "version": ">= 3.3", "role": "Imports" }, { "package": "Mercator", "role": "Imports" }, { "package": "rgl", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "Polychrome", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "ape", "role": "Suggests" }, { "package": "PCDimension", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-08", "n": 1 } ], "_tags": [ { "name": "0.9.1", "date": "2026-02-17" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 184, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RPointCloud" }, "_devurl": "https://github.com/r-forge/oompa", "_searchresults": 14, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/RPointCloud.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.6.2", "date": "2024-06-25" }, { "version": "0.8.0", "date": "2024-08-19" }, { "version": "0.9.1", "date": "2026-02-17" } ], "_exports": [ "angleMeans", "cutoff", "cutoffSignificant", "Cycle", "cycleSupport", "disentangle", "EBexpo", "ExpoFit", "Feature", "getCycle", "hist", "image", "LDPC", "lines", "LoopCircos", "LoopFeature", "plot", "points", "Projection", "tailHisto", "takens", "voidFeature", "voidPlot" ], "_datasets": [ { "name": "AML10.node287", "title": "CyTOF Data", "object": "cytof", "file": "cytof.rda", "class": [ "matrix", "array" ], "fields": [ "CD45RA", "CD133", "CD47", "p21", "CD90", "CycA", "CycB", "PCNA", "Ki-67", "pRb", "CD99", "CD13", "pCDK1", "H2AX", "cPARP", "pS6", "pH3", "DNA-2" ], "rows": 214, "table": true, "tojson": true }, { "name": "AML10.node287.rips", "title": "CyTOF Data", "object": "cytof", "file": "cytof.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "Arip", "title": "CyTOF Data", "object": "cytof", "file": "cytof.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "clinical", "title": "Chronic Lymphocytic Leukemia Clinical Data", "object": "CLL", "file": "CLL.rda", "class": [ "matrix", "array" ], "fields": [ "AgeAtDx", "Sex", "Race", "mutation.status", "Light.chain.subtype", "Zap70Protein", "Rai.Stage", "CatRAI", "Serum.beta.2.microglobulin", "LogB2M", "CatB2M", "Serum.LDH", "LogLDH", "White.blood.count", "LogWBC", "CatWBC", "CatCD38", "Hypogammaglobulinemia", "Massive.Splenomegaly", "Matutes", "Hemoglobin", "Platelets", "Prolymphocytes", "stat13", "stat11", "stat12", "stat17", "Dohner", "Purity" ], "rows": 266, "table": true, "tojson": true }, { "name": "daisydist", "title": "Chronic Lymphocytic Leukemia Clinical Data", "object": "CLL", "file": "CLL.rda", "class": [ "dissimilarity", "dist" ], "fields": [], "table": false, "tojson": false }, { "name": "rip", "title": "Single Cell Data on T Regulatory (Treg) Cells", "object": "treg", "file": "treg.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "ripdiag", "title": "Chronic Lymphocytic Leukemia Clinical Data", "object": "CLL", "file": "CLL.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "tmat", "title": "Single Cell Data on T Regulatory (Treg) Cells", "object": "treg", "file": "treg.rda", "class": [ "dist" ], "fields": [], "table": false, "tojson": false }, { "name": "treg", "title": "Single Cell Data on T Regulatory (Treg) Cells", "object": "treg", "file": "treg.rda", "class": [ "matrix", "array" ], "fields": [ "268440_P1_P2", "531263_P1_P2", "668604_P1_P2", "6189_P1_P2", "558197_P1_P2", "733801_P1_P2", "519449_P1_P2", "296219_P1_P2", "451237_P1_P2", "712990_P1_P2", "284381_P1_P2", "732232_P1_P2", "265665_P1_P2", "297289_P1_P2", "221095_P1_P2", "338512_P1_P2", "595862_P1_P2", "354686_P1_P2", "180999_P1_P2", "105858_P1_P2", "273227_P1_P2", "370054_P1_P2", "699368_P1_P2", "338198_P1_P2", "649397_P1_P2", "563394_P1_P2", "77973_P1_P2", "338549_P1_P2", "793246_P1_P2", "718531_P1_P2", "375591_P1_P2", "769263_P1_P2", "384026_P1_P2", "254446_P1_P2", "546773_P1_P2", "103561_P3_P4", "39928_P3_P4", "67822_P3_P4", "53568_P3_P4", "43528_P3_P4", "643975_P3_P4", "92688_P3_P4", "500351_P3_P4", "808389_P3_P4", "603482_P3_P4", "818841_P3_P4", "53703_P3_P4", "708340_P3_P4", "407739_P3_P4", "811732_P3_P4", "580729_P3_P4", "169773_P3_P4", "760426_P3_P4", "263355_P3_P4", "51144_P3_P4", "604865_P3_P4", "640130_P3_P4", "758220_P5_P6", "78753_P5_P6", "600308_P5_P6", "768140_P5_P6", "225530_P5_P6", "371043_P5_P6", "540265_P5_P6", "659373_P5_P6", "578797_P5_P6", "801782_P5_P6", "245010_P5_P6", "212008_P5_P6", "242861_P5_P6", "412299_P5_P6", "548607_P5_P6", "636300_P5_P6", "799351_P5_P6", "43565_P5_P6", "733183_P5_P6", "609924_P5_P6", "703165_P5_P6", "462084_P5_P6", "776090_P5_P6", "304214_P5_P6", "653248_P5_P6", "117385_P5_P6", "789365_P5_P6", "717008_P5_P6", "5958_P5_P6", "703965_P5_P6", "844253_P7_P8", "182594_P7_P8", "84693_P7_P8", "424087_P7_P8", "706798_P7_P8", "733788_P7_P8", "768661_P7_P8", "239054_P7_P8", "166747_P7_P8", "218819_P7_P8", "443671_P7_P8", "424479_P7_P8", "117618_P7_P8", "448708_P7_P8", "286721_P7_P8", "200202_P7_P8", "565847_P7_P8", "652423_P9_P10", "299418_P9_P10", "874029_P9_P10", "347746_P9_P10", "186169_P9_P10", "89136_P9_P10", "104463_P9_P10", "111600_P9_P10", "800690_P9_P10", "604733_P9_P10", "498436_P9_P10", "843339_P9_P10", "17635_P9_P10", "215917_P9_P10", "34085_P9_P10", "402164_P9_P10", "508405_P9_P10", "688001_P9_P10", "632323_P9_P10", "704202_P9_P10", "671556_P9_P10", "715310_P9_P10", "546556_P9_P10", "635362_P9_P10", "105962_P9_P10", "361109_P9_P10", "454683_P9_P10", "344733_P9_P10", "779361_P9_P10", "225471_P9_P10", "454078_P9_P10", "709999_P9_P10", "133846_P9_P10", "64298_P9_P10", "86546_P9_P10", "507163_P9_P10", "529305_P9_P10", "60846_P9_P10", "159978_P9_P10", "795029_P9_P10", "84146_P9_P10", "551848_P9_P10", "677651_P9_P10", "844634_P11_P12", "598926_P11_P12", "684787_P11_P12", "268463_P11_P12", "514312_P11_P12", "862119_P11_P12", "840561_P11_P12", "538601_P11_P12", "735055_P11_P12", "822099_P11_P12", "497487_P11_P12", "125712_P11_P12", "557246_P11_P12", "317070_P11_P12", "590001_P11_P12", "92588_P11_P12", "766619_P13_P14", "57420_P13_P14", "523210_P13_P14", "224877_P13_P14", "853885_P13_P14", "630895_P13_P14", "565597_P13_P14", "44412_P13_P14", "81332_P13_P14", "720087_P13_P14", "662634_P13_P14", "90366_P13_P14", "687460_P13_P14", "858880_P13_P14", "16316_P13_P14", "312885_P13_P14", "711714_P13_P14", "769394_P13_P14", "117455_P13_P14", "11574_P13_P14", "670192_P13_P14", "457132_P13_P14", "402604_P13_P14", "669962_P13_P14", "720335_P15_P16", "858068_P15_P16", "275888_P15_P16", "781484_P15_P16", "736285_P15_P16", "23295_P15_P16", "268754_P15_P16", "330506_P15_P16", "685028_P15_P16", "689627_P15_P16", "354652_P15_P16", "861303_P15_P16", "110340_P15_P16", "617692_P15_P16", "437730_P15_P16", "330957_P15_P16", "834625_P15_P16", "375248_P15_P16", "211299_P15_P16", "373102_P15_P16", "470891_P15_P16", "249025_P15_P16", "83958_P15_P16", "511326_P15_P16", "370328_P15_P16", "173513_P15_P16", "412270_P15_P16", "614327_P15_P16", "608694_P15_P16", "557430_P15_P16", "85897_P15_P16", "31669_P15_P16", "99385_P15_P16", "394256_P15_P16", "59626_P15_P16", "589067_P15_P16", "534408_P15_P16", "218908_P15_P16", "727456_P15_P16", "695484_P15_P16", "546571_P15_P16", "513020_P15_P16", "860263_P15_P16", "684370_P15_P16", "884209_P15_P16", "246118_P15_P16", "164005_P15_P16", "835788_P15_P16", "394830_P15_P16", "835105_P15_P16", "614145_P15_P16", "34604_P15_P16", "816260_P15_P16", "16849_P15_P16", "525222_P15_P16", "703158_P15_P16", "831625_P15_P16", "158820_P15_P16", "305737_P15_P16", "511942_P15_P16", "832281_P15_P16", "485640_P15_P16", "843543_P15_P16", "109352_P15_P16", "677460_P15_P16", "398662_P15_P16", "221434_P15_P16", "502568_P15_P16" ], "rows": 538, "table": true, "tojson": true } ], "_help": [ { "page": "m01-CLL", "title": "Chronic Lymphocytic Leukemia Clinical Data", "topics": [ "clinical", "CLL-data", "daisydist", "ripdiag" ] }, { "page": "m04-Cycle-class", "title": "'Cycle' Objects For Visualizing Topological Data Analysis Results", "topics": [ "Cycle", "Cycle-class", "cycleSupport", "getCycle", "lines,Cycle-method", "plot,Cycle,matrix-method" ] }, { "page": "m02-cytof", "title": "CyTOF Data", "topics": [ "AML10.node287", "AML10.node287.rips", "Arip", "cytof-data" ] }, { "page": "m03-disentangle", "title": "Disentangling Rips Diagrams From Their Initial Data Coordinates", "topics": [ "disentangle" ] }, { "page": "m07-EBexpo-class", "title": "The 'EBexpo' Class", "topics": [ "cutoff", "EBexpo", "EBexpo-class", "hist,EBexpo-method", "plot,EBexpo,missing-method" ] }, { "page": "m06-ExpoFit-class", "title": "The 'ExpoFit' Class", "topics": [ "ExpoFit", "ExpoFit-class", "plot,ExpoFit,missing-method" ] }, { "page": "m05-Feature-class", "title": "'Feature' Objects For Visualizing Topological Data Anal;ysis Results", "topics": [ "Feature", "Feature-class", "plot,Feature,matrix-method", "points,Feature-method" ] }, { "page": "m3-ldpc", "title": "Local Dimension of Point Clouds", "topics": [ "LDPC", "takens" ] }, { "page": "m08-LoopCircos-Class", "title": "The 'LoopCircos' Class", "topics": [ "angleMeans", "image,LoopCircos-method", "LoopCircos", "LoopCircos-class" ] }, { "page": "m12-LoopFeature", "title": "'LoopFeature' Objects For Visualizing Features That Define Loops", "topics": [ "image,LoopFeature-method", "LoopFeature", "LoopFeature-class", "plot,LoopFeature,character-method", "plot,LoopFeature,missing-method" ] }, { "page": "m11-Projection", "title": "'Projection' Objects For Visualizing 3D Topological Data Analysis Results in 2D", "topics": [ "image,Projection-method", "plot,Projection,missing-method", "Projection", "Projection-class" ] }, { "page": "m10-tailHisto", "title": "Function to extract the right tail of a histogram for display purposes.", "topics": [ "tailHisto" ] }, { "page": "m00-immune", "title": "Single Cell Data on T Regulatory (Treg) Cells", "topics": [ "rip", "tmat", "treg", "treg-data" ] }, { "page": "m09-voids.R", "title": "3D Scatter Plots of Cycles and Features", "topics": [ "voidFeature", "voidPlot", "voids" ] } ], "_rundeps": [ "ade4", "askpass", "base64enc", "BH", "Biobase", "BiocGenerics", "bslib", "cachem", "changepoint", "circlize", "ClassComparison", "ClassDiscovery", "cli", "clue", "cluster", "colorspace", "cpm", "cpp11", "dendextend", "digest", "evaluate", "farver", "fastmap", "flexmix", "FNN", "fontawesome", "fs", "generics", "ggplot2", "GlobalOptions", "glue", "gridExtra", "gtable", "here", "highr", "htmltools", "htmlwidgets", "igraph", "isoband", "jquerylib", "jsonlite", "kernlab", "KernSmooth", "knitr", "kohonen", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "mclust", "memoise", "Mercator", "mime", "modeltools", "movMF", "nnet", "oompaBase", "oompaData", "openssl", "PCDimension", "pixmap", "pkgconfig", "png", "Polychrome", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppTOML", "reticulate", "rgl", "rlang", "rmarkdown", "rprojroot", "RSpectra", "Rtsne", "S7", "sass", "scales", "scatterplot3d", "shape", "skmeans", "slam", "sp", "sys", "TDA", "Thresher", "tinytex", "umap", "vctrs", "viridis", "viridisLite", "withr", "xfun", "yaml", "zoo" ], "_vignettes": [ { "source": "cytof.Rmd", "filename": "cytof.html", "title": "RPointCloud: A Mass Cytometry Example", "author": "Kevin R. Coombes and Jake Reed", "engine": "knitr::rmarkdown", "headings": [ "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)" ], "created": "2024-06-26 02:42:08", "modified": "2026-02-17 21:10:08", "commits": 2 }, { "source": "clinical.Rmd", "filename": "clinical.html", "title": "RPointCloud: CLL Clinical Data", "author": "Kevin R. Coombes and Jake Reed", "engine": "knitr::rmarkdown", "headings": [ "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)" ], "created": "2024-06-26 02:42:08", "modified": "2026-02-17 21:10:08", "commits": 3 }, { "source": "treg.Rmd", "filename": "treg.html", "title": "RPointCloud: Regulatory T Cells", "author": "Kevin R. Coombes", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2024-06-26 02:42:08", "modified": "2026-02-17 21:10:08", "commits": 2 } ], "_score": 2.6232492903979003, "_indexed": true, "_nocasepkg": "rpointcloud", "_universes": [ "cran", "r-forge" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.9.1", "date": "2026-05-18T09:32:20.000Z", "distro": "noble", "commit": "31f352887abc633c0cc765d29df9a700618ce072", "fileid": "76f47e359500a1830cb084cfb93ad90038d8d4119ee46e6df76719c2fd7103d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26024827956" }, { "r": "4.6.0", "os": "linux", "version": "0.9.1", "date": "2026-05-18T09:32:38.000Z", "distro": "noble", "commit": "31f352887abc633c0cc765d29df9a700618ce072", "fileid": "fa9823e935ba3617c20fc2924cc0140317b9b1ebf0de378cf29fde2d01b6c038", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26024827956" }, { "r": "4.6.0", "os": "wasm", "version": "0.9.1", "date": "2026-06-02T16:00:27.000Z", "commit": "31f352887abc633c0cc765d29df9a700618ce072", "fileid": "8e0c555e766895f53ab367500da5486b62ca5c13568fdf395781abf7b7343213", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26024827956" } ] }