{ "_id": "6ad46f79dc7ca4d810c6cb7c", "Package": "flowPlots", "Type": "Package", "Version": "1.61.0", "Title": "flowPlots: analysis plots and data class for gated flow\ncytometry data", "Description": "Graphical displays with embedded statistical tests for\ngated ICS flow cytometry data, and a data class which stores\n\"stacked\" data and has methods for computing summary measures\non stacked data, such as marginal and polyfunctional degree\ndata.", "Author": "N. Hawkins, S. Self", "Maintainer": "N. Hawkins ", "LazyData": "yes", "License": "Artistic-2.0", "biocViews": "ImmunoOncology, FlowCytometry, CellBasedAssays,\nVisualization, DataRepresentation", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:14 UTC", "RemoteUrl": "https://github.com/bioc/flowPlots", "RemoteRef": "HEAD", "RemoteSha": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-18 06:51:44 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "flowPlots_1.61.0.tar.gz", "_fileid": "https://r2.ropensci.org/77d921e564fd880d1e3553a71063e74e3b1510c16a1e1f5815555c078fa94bc3", "_filesize": 625396, "_sha256": "77d921e564fd880d1e3553a71063e74e3b1510c16a1e1f5815555c078fa94bc3", "_expires": "2027-01-26T07:04:23.000Z", "_created": "2026-10-18T06:51:44.000Z", "_published": "2026-10-18T07:04:25.300Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39105394356", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 4, "note": 15 }, "_upstream": "https://github.com/bioc/flowPlots", "_commit": { "id": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379714 }, "_maintainer": { "name": "N. Hawkins", "email": "hawkins@fhcrc.org" }, "_distro": "resolute", "_jobs": [ { "job": 117610522729, "time": 106, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12128800209" }, { "job": 117610522706, "time": 209, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12128511954" }, { "job": 117610522725, "time": 134, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12128541526" }, { "job": 117610522710, "time": 105, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12128193975" }, { "job": 117610522677, "time": 98, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12128711590" }, { "job": 117610088538, "time": 138, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12128591076" }, { "job": 117610522671, "time": 75, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12127882425" }, { "job": 117610522700, "time": 68, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12127823892" }, { "job": 117610522722, "time": 68, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12127299996" }, { "job": 117610522680, "time": 66, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12127858813" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.13.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "vcd", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.61.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.60.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "immunooncology", "flowcytometry", "cellbasedassays", "visualization", "datarepresentation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 478, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 544, "source": "https://www.bioconductor.org/packages/stats/bioc/flowPlots" }, "_searchresults": 6, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/flowPlots.html", "extra/manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "computeMarginalData", "computeMarkers", "computePFDData", "computePFDGroupStatsList", "computePFDPartsData", "computeProfileData", "GroupListBoxplot", "legendPFDStatsGroupNames", "makeBarplotData", "makeDataList", "makeTernaryData", "marginalData", "marginalData<-", "markers", "markers<-", "pfdData", "pfdData<-", "pfdPartsData", "pfdPartsData<-", "profileData", "profileData<-", "readStackedData", "stackedData", "stackedData<-" ], "_datasets": [ { "name": "adultsNeonates", "title": "The adultsNeonates example data set of \"stacked\" data.", "object": "adultsNeonates", "class": [ "data.frame" ], "fields": [ "id", "group", "stim", "concGroup", "cell", "percentAll", "count", "totalCount", "percentReactive", "cytCombo" ], "rows": 6912, "table": true, "tojson": true }, { "name": "marginalDF", "title": "An example of marginalData", "object": "marginalDF", "class": [ "data.frame" ], "fields": [ "TNFa", "IL6", "IL12", "IFNa", "AnyMarker", "stim", "concGroup", "cell", "groups", "subjectId", "group" ], "rows": 432, "table": true, "tojson": true }, { "name": "markerMatrix", "title": "An example of the markers data.", "object": "markerMatrix", "class": [ "matrix", "array" ], "fields": [ "TNFa", "IL6", "IL12", "IFNa" ], "rows": 16, "table": true, "tojson": true }, { "name": "pfdDF", "title": "An example of pfdData", "object": "pfdDF", "class": [ "data.frame" ], "fields": [ "PFD1", "PFD2", "PFD3", "PFD4", "stim", "concGroup", "cell", "groups", "subjectId", "group" ], "rows": 432, "table": true, "tojson": true }, { "name": "pfdPartsList", "title": "An example of pfdPartsData", "object": "pfdPartsList", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "profileDF", "title": "An example of profileData", "object": "profileDF", "class": [ "data.frame" ], "fields": [ "TNFa+IL6+IL12+IFNa+", "TNFa+IL6+IL12+IFNa-", "TNFa+IL6+IL12-IFNa+", "TNFa+IL6+IL12-IFNa-", "TNFa+IL6-IL12+IFNa+", "TNFa+IL6-IL12+IFNa-", "TNFa+IL6-IL12-IFNa+", "TNFa+IL6-IL12-IFNa-", "TNFa-IL6+IL12+IFNa+", "TNFa-IL6+IL12+IFNa-", "TNFa-IL6+IL12-IFNa+", "TNFa-IL6+IL12-IFNa-", "TNFa-IL6-IL12+IFNa+", "TNFa-IL6-IL12+IFNa-", "TNFa-IL6-IL12-IFNa+", "TNFa-IL6-IL12-IFNa-", "stim", "concGroup", "cell", "groups", "subjectId", "group" ], "rows": 432, "table": true, "tojson": true } ], "_help": [ { "page": "adultsNeonates", "title": "The adultsNeonates example data set of \"stacked\" data.", "topics": [ "adultsNeonates" ] }, { "page": "computeMarginalData-methods", "title": "Method computeMarginalData from Class \"StackedData\"", "topics": [ "computeMarginalData", "computeMarginalData,StackedData,character,character,character,character-method", "computeMarginalData-methods" ] }, { "page": "computeMarkers-methods", "title": "Method computeMarkers from Class \"StackedData\"", "topics": [ "computeMarkers", "computeMarkers,character,logical-method", "computeMarkers-methods" ] }, { "page": "computePFDData-methods", "title": "Method computePFDData from Class \"StackedData\"", "topics": [ "computePFDData", "computePFDData,StackedData,character,character,character,character-method", "computePFDData-methods" ] }, { "page": "computePFDGroupStatsList", "title": "Compute Group Stats on PFD Data to Be Used In a Legend", "topics": [ "computePFDGroupStatsList" ] }, { "page": "computePFDPartsData-methods", "title": "Method computePFDPartsData from Class \"StackedData\"", "topics": [ "computePFDPartsData", "computePFDPartsData,StackedData,character,character,character,character-method", "computePFDPartsData-methods" ] }, { "page": "computeProfileData-methods", "title": "Method computeProfileData from Class \"StackedData\"", "topics": [ "computeProfileData", "computeProfileData,StackedData,character,character,character,character-method", "computeProfileData-methods" ] }, { "page": "GroupListBoxplot", "title": "A Boxplot Function With Embedded Statistical Tests for Comparing Groups", "topics": [ "GroupListBoxplot" ] }, { "page": "legendPFDStatsGroupNames", "title": "Create Group Names With Embedded Stats to Use in a Plot Legend", "topics": [ "legendPFDStatsGroupNames" ] }, { "page": "makeBarplotData", "title": "Prepare Profile Data for a Call to Barplot()", "topics": [ "makeBarplotData" ] }, { "page": "makeDataList", "title": "Prepare Data in a Data Frame for a Call to GroupListBoxplot()", "topics": [ "makeDataList" ] }, { "page": "makeTernaryData", "title": "Prepare PFD Data for a Call to ternaryplot()", "topics": [ "makeTernaryData" ] }, { "page": "marginalData-methods", "title": "Method marginalData from Class \"StackedData\"", "topics": [ "marginalData", "marginalData,StackedData-method", "marginalData-methods", "marginalData<-", "marginalData<-,StackedData-method", "marginalData<--methods" ] }, { "page": "marginalDF", "title": "An example of marginalData", "topics": [ "marginalDF" ] }, { "page": "markerMatrix", "title": "An example of the markers data.", "topics": [ "markerMatrix" ] }, { "page": "markers-methods", "title": "Method markers from Class \"StackedData\"", "topics": [ "markers", "markers,StackedData-method", "markers-methods", "markers<-", "markers<-,StackedData-method", "markers<--methods" ] }, { "page": "pfdData-methods", "title": "Method pfdData from Class \"StackedData\"", "topics": [ "pfdData", "pfdData,StackedData-method", "pfdData-methods", "pfdData<-", "pfdData<-,StackedData-method", "pfdData<--methods" ] }, { "page": "pfdDF", "title": "An example of pfdData", "topics": [ "pfdDF" ] }, { "page": "pfdPartsData-methods", "title": "Method pfdPartsData from Class \"StackedData\"", "topics": [ "pfdPartsData", "pfdPartsData,StackedData-method", "pfdPartsData-methods", "pfdPartsData<-", "pfdPartsData<-,StackedData-method", "pfdPartsData<--methods" ] }, { "page": "pfdPartsList", "title": "An example of pfdPartsData", "topics": [ "pfdPartsList" ] }, { "page": "profileData-methods", "title": "Method profileData from Class \"StackedData\"", "topics": [ "profileData", "profileData,StackedData-method", "profileData-methods", "profileData<-", "profileData<-,StackedData-method", "profileData<--methods" ] }, { "page": "profileDF", "title": "An example of profileData", "topics": [ "profileDF" ] }, { "page": "readStackedData-methods", "title": "Method readStackedData from Class \"StackedData\"", "topics": [ "readStackedData", "readStackedData,character-method" ] }, { "page": "StackedData-class", "title": "Class \"StackedData\"", "topics": [ "StackedData", "StackedData-class" ] }, { "page": "stackedData-methods", "title": "Method stackedData from Class \"StackedData\"", "topics": [ "stackedData", "stackedData,StackedData-method", "stackedData-methods", "stackedData<-", "stackedData<-,StackedData-method", "stackedData<--methods" ] } ], "_rundeps": [], "_vignettes": [ { "source": "flowPlots.Rnw", "filename": "flowPlots.pdf", "title": "Plots with Embedded Tests for Gated Flow Cytometry Data", "engine": "utils::Sweave", "headings": [ "Introduction", "Plotting the data: boxplots, ternary plot, bar plot", "A Boxplot Example to Illustrate Multiple Groups and Point Colors", "The StackedData Class", "Using the StackedData Class", "Acknowledgments" ], "created": "2013-11-01 20:17:44", "modified": "2013-11-01 20:17:44", "commits": 1 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "flowplots", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.61.0", "date": "2026-10-18T06:55:15.000Z", "distro": "resolute", "commit": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "fileid": "https://r2.ropensci.org/0c563ebe39681013a19083250ca5efa3c29bc67ad57df5dd7392ab6a5518ca20", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39105394356" }, { "r": "4.6.1", "os": "linux", "version": "1.61.0", "date": "2026-10-18T06:54:02.000Z", "distro": "resolute", "commit": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "fileid": "https://r2.ropensci.org/2242da10ff34022a9cd5a7540085528bc9fa9d1f0b82a8de95c1b0c3cd934c20", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39105394356" }, { "r": "4.5.3", "os": "mac", "version": "1.61.0", "date": "2026-10-18T07:03:44.000Z", "commit": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "fileid": "https://r2.ropensci.org/94bf3819e61c3b66e501ab2998daf876d86d0bfa42a8f6c0d4f92a247d9f7b36", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39105394356" }, { "r": "4.6.1", "os": "mac", "version": "1.61.0", "date": "2026-10-18T06:59:38.000Z", "commit": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "fileid": "https://r2.ropensci.org/8639dd1c49ea7aac145ab0ac555f7ac8778e614b9591291d37a13800df9c1964", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39105394356" }, { "r": "4.6.0", "os": "wasm", "version": "1.61.0", "date": "2026-10-18T06:53:18.000Z", "commit": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "fileid": "https://r2.ropensci.org/04222f6c098d696303c4138a6edd504ec6528f2ea7615be9eee1bc909b808663", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39105394356" }, { "r": "4.7.0", "os": "win", "version": "1.61.0", "date": "2026-10-18T06:52:46.000Z", "commit": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "fileid": "https://r2.ropensci.org/c41f9b7fc498e637cd05fb954bd6405fe358d5d264705cbdf90502d0c71e81c2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39105394356" }, { "r": "4.5.3", "os": "win", "version": "1.61.0", "date": "2026-10-18T06:52:48.000Z", "commit": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "fileid": "https://r2.ropensci.org/3749cca7f9b3cc63aee8ae903dc224147a9b10f174fb9dc492a1c1e88e7ad53c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39105394356" }, { "r": "4.6.1", "os": "win", "version": "1.61.0", "date": "2026-10-18T06:52:46.000Z", "commit": "ef7cb55ea36126aeb25742f08ae38c2039b08113", "fileid": "https://r2.ropensci.org/d23361d7cd347f39f4111f011b88f4ab93a79f79b2f6c9e8b6025256a1fb16af", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39105394356" } ] }