{ "_id": "6a195fc2acfb0bcc41de5661", "Package": "escheR", "Title": "Unified multi-dimensional visualizations with Gestalt principles", "Version": "1.12.0", "Authors@R": "c(\nperson(\"Boyi\", \"Guo\",\nemail = \"boyi.guo.work@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-2950-2349\")),\nperson(c(\"Stephanie\", \"C.\"), \"Hicks\", role = c(\"aut\"),\nemail = \"shicks19@jhu.edu\",\ncomment = c(ORCID = \"0000-0002-7858-0231\")),\nperson(c(\"Erik\", \"D.\"), \"Nelson\",\nemail = \"erik.nelson116@gmail.com\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-8477-0982\"))\n)", "Description": "The creation of effective visualizations is a fundamental\ncomponent of data analysis. In biomedical research, new\nchallenges are emerging to visualize multi-dimensional data in\na 2D space, but current data visualization tools have limited\ncapabilities. To address this problem, we leverage Gestalt\nprinciples to improve the design and interpretability of\nmulti-dimensional data in 2D data visualizations, layering\naesthetics to display multiple variables. The proposed\nvisualization can be applied to spatially-resolved\ntranscriptomics data, but also broadly to data visualized in 2D\nspace, such as embedding visualizations. We provide this open\nsource R package escheR, which is built off of the\nstate-of-the-art ggplot2 visualization framework and can be\nseamlessly integrated into genomics toolboxes and workflows.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "biocViews": "Spatial, SingleCell, Transcriptomics, Visualization,\nSoftware", "BugReports": "https://github.com/boyiguo1/escheR/issues", "URL": "https://github.com/boyiguo1/escheR", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:00:23 UTC", "RemoteUrl": "https://github.com/bioc/escheR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 08:05:40 UTC", "User": "root" }, "Author": "Boyi Guo [aut, cre] (ORCID: ),\nStephanie C. Hicks [aut] (ORCID:\n),\nErik D. Nelson [ctb] (ORCID: )", "Maintainer": "Boyi Guo ", "MD5sum": "f7a0cba4e4efd0d82d549280954fe328", "_user": "bioc-release", "_type": "src", "_file": "escheR_1.12.0.tar.gz", "_fileid": "daa63c013e23d721fd28fefcf7950f16442586264719bed9891a5aeedad5b25b", "_filesize": 3518742, "_sha256": "daa63c013e23d721fd28fefcf7950f16442586264719bed9891a5aeedad5b25b", "_created": "2026-05-29T08:05:40.000Z", "_published": "2026-05-29T09:43:30.827Z", "_jobs": [ { "job": 78462424440, "time": 256, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7286111486" }, { "job": 78462424468, "time": 347, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7286135999" }, { "job": 78462424464, "time": 401, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7286151712" }, { "job": 78462424454, "time": 206, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7287771525" }, { "job": 78462424477, "time": 231, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7287778956" }, { "job": 78461420470, "time": 430, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7286040772" }, { "job": 78462424449, "time": 198, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7286095706" }, { "job": 78462424443, "time": 369, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7286143123" }, { "job": 78462424463, "time": 335, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7286133159" }, { "job": 78462424517, "time": 364, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7286141591" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625574313", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/escheR", "_commit": { "id": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381223 }, "_maintainer": { "name": "Boyi Guo", "email": "boyi.guo.work@gmail.com", "login": "boyiguo1", "orcid": "0000-0003-2950-2349", "twitter": "@BoyiGuo", "description": "Biostatistician, Omics data scientist", "uuid": 16565218 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "ggplot2", "role": "Depends" }, { "package": "R", "version": ">= 4.3", "role": "Depends" }, { "package": "SpatialExperiment", "version": ">= 1.6.1", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "STexampleData", "role": "Suggests" }, { "package": "BumpyMatrix", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "ggpubr", "role": "Suggests" }, { "package": "scran", "role": "Suggests" }, { "package": "scater", "role": "Suggests" }, { "package": "scuttle", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" }, { "package": "hexbin", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.13.0", "bioc": "3.24" }, { "branch": "release", "version": "1.12.0", "bioc": "3.23" } ], "_topics": [ "spatial", "singlecell", "transcriptomics", "visualization", "software", "multidimensional", "single-cell", "spatial-omics" ], "_stars": 8, "_contributors": [ { "user": "boyiguo1", "count": 201, "uuid": 16565218 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 440, "source": "https://www.bioconductor.org/packages/stats/bioc/escheR" }, "_devurl": "https://github.com/boyiguo1/escher", "_searchresults": 290, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/escheR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/boyiguo1/escher", "_realowner": "bioc", "_cranurl": false, "_exports": [ "add_fill", "add_fill_bin", "add_ground", "add_ground_bin", "add_symbol", "make_escheR" ], "_help": [ { "page": "dot-contain_reserved_col_name", "title": "Check if rowData(spe) contains reserved name", "topics": [ ".contain_reserved_col_name" ] }, { "page": "add_fill", "title": "Adding fill to highlight the figure in the spatial map", "topics": [ "add_fill", "add_fill_bin" ] }, { "page": "add_ground", "title": "Adding border to highlight the ground in the spatial map", "topics": [ "add_ground", "add_ground_bin" ] }, { "page": "add_symbol", "title": "Adding symbols to each spot in the spatial map", "topics": [ "add_symbol" ] }, { "page": "make_escheR", "title": "Create a new spatial map for spatial transcriptomics data", "topics": [ "make_escheR", "make_escheR.data.frame", "make_escheR.SingleCellExperiment", "make_escheR.SpatialExperiment" ] } ], "_pkglogo": "https://github.com/bioc/escheR/raw/RELEASE_3_23/man/figures/logo.png", "_readme": "https://github.com/bioc/escheR/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "askpass", "Biobase", "BiocFileCache", "BiocGenerics", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "farver", "fastmap", "filelock", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "httr2", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "magick", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "openssl", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rjson", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SingleCellExperiment", "SparseArray", "SpatialExperiment", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "more_than_visium.Rmd", "filename": "more_than_visium.html", "title": "Beyond Sequence-based Spatially-Resolved Data", "engine": "knitr::rmarkdown", "headings": [ "Visualized Dimensionality Reduced Embedding with SingleCellExperiment", "SpatialExperiment inherits SingleCellExperiment", "Hex Binning", "Image-based SpatialExperiment Object", "seqFISH", "SlideSeqV2", "Beyond Bioconductor Eco-system", "Session information" ], "created": "2023-09-20 00:38:11", "modified": "2023-11-14 03:23:00", "commits": 5 }, { "source": "SRT_eg.Rmd", "filename": "SRT_eg.html", "title": "Getting Started with escheR", "author": "Boyi Guo, Stephanie C. Hicks", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Input data format", "Making escheR Plot", "Load Packages", "Preparing example data", "Set up an escheR plot", "Adding layers", "Customize escheR Plot", "Choosing Color Palette for add_fill and add_ground", "Coninuous variable (gene expression) vs Categorical variable (Spatial Domains)", "Categorical variable Vs Categorical variable", "Guidance in choosing bivariate color palette", "Adjusting aesthetics", "Show a subset of levels", "Multi-sample Figure", "Save escheR plot", "Session information" ], "created": "2023-03-24 02:16:01", "modified": "2024-01-12 21:28:27", "commits": 14 } ], "_score": 7.143639235274543, "_indexed": false, "_nocasepkg": "escher", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/escheR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.12.0", "date": "2026-05-29T08:09:46.000Z", "distro": "noble", "commit": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "fileid": "cc4011172c6e1b2e78ea2cbc20c7e7b7250485ccdf307a65788655aa0f6a997f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625574313" }, { "r": "4.6.0", "os": "linux", "version": "1.12.0", "date": "2026-05-29T08:10:36.000Z", "distro": "noble", "commit": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "fileid": "09ca489b1fc45d44d4ed2cdb8291d414b86b20ed3bcfa4a168cae7101753c067", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625574313" }, { "r": "4.5.3", "os": "mac", "version": "1.12.0", "date": "2026-05-29T09:40:53.000Z", "commit": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "fileid": "ef2dd48fb0cce848bba3cc8c20a544d795b5e452cf161e521c24768a805b29e3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625574313" }, { "r": "4.6.0", "os": "mac", "version": "1.12.0", "date": "2026-05-29T09:41:17.000Z", "commit": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "fileid": "7be4a8a7f2545e0c83f1aef51c3cd36a48bde99151013417e97e365256faf199", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625574313" }, { "r": "4.6.0", "os": "wasm", "version": "1.12.0", "date": "2026-05-29T08:09:33.000Z", "commit": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "fileid": "4f19262993a7b37ab533ed5c2f1bbda0f650862622187b6180afdde929c63de9", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625574313" }, { "r": "4.7.0", "os": "win", "version": "1.12.0", "date": "2026-05-29T08:09:50.000Z", "commit": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "fileid": "611ae2658767e1ce3fbf16370096918f7a13df0c4abcad4cc2ea338b3f4a3c95", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625574313" }, { "r": "4.5.3", "os": "win", "version": "1.12.0", "date": "2026-05-29T08:10:01.000Z", "commit": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "fileid": "5d7e03bbe4bd032d991503159307334510de7530f1911293116c506711d3c82e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625574313" }, { "r": "4.6.0", "os": "win", "version": "1.12.0", "date": "2026-05-29T08:10:05.000Z", "commit": "a5e8f249b969079f09ac5e09204b0ac934c94c5c", "fileid": "3e3e58b1110edbc46241c9b5012ada3ec0ef826d477b683ce9c3033a4865d353", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625574313" } ] }