{ "_id": "6ad8890669e274306bae97e5", "Package": "palettome", "Title": "Hierarchy-Aware, Interactively Editable Color Palettes for\nClusters", "Version": "1.0.1", "Authors@R": "person(\"Chenbin\", \"Huang\", email = \"chenbin.huang@emory.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-2179-2217\"))", "Description": "Assigns perceptually-informed color palettes to clustered\ndata (e.g. scRNA-seq clusters / cell subtypes from 'Seurat' or\nplain UMAP coordinate tables), where clusters that belong to\nthe same \"family\" (e.g. subtypes of T cells) can be colored\neither harmoniously (shared hue, varying shade) or with maximal\ncontrast (with family membership encoded via a secondary\nchannel). Families can be auto-detected from embedding-space\nhierarchical clustering or supplied explicitly, and every\ngenerated color remains individually overridable, with manual\noverrides preserved across regeneration. Colors are constructed\nin the HCL space as in Zeileis et al. (2020)\n, separated using the CIEDE2000\ncolor difference of Sharma, Wu and Dalal (2005)\n, and checked for color-vision\ndeficiency using the simulation of Machado, Oliveira and\nFernandes (2009) . Core algorithms\nhave no UI dependencies; an optional interactive 'shiny' UI is\nprovided separately.", "License": "Apache License (== 2.0)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "URL": "https://github.com/thisishcb/Palettome", "BugReports": "https://github.com/thisishcb/Palettome/issues", "Repository": "https://thisishcb.r-universe.dev", "Date/Publication": "2026-10-20 19:57:32 UTC", "RemoteUrl": "https://github.com/thisishcb/palettome", "RemoteRef": "HEAD", "RemoteSha": "6683a9e84e971f5a33c7ee1c645fd25265701bb5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-21 09:38:00 UTC", "User": "root" }, "Author": "Chenbin Huang [aut, cre] (ORCID:\n)", "Maintainer": "Chenbin Huang ", "_user": "thisishcb", "_type": "src", "_file": "palettome_1.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/df29529e2334bdb2eaca586b4c728e5fe2366ac76a179cba0cf3dbbddd0ec229", "_filesize": 1287015, 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Informatics | Emory University ", "uuid": 24517165, "orcid": "0000-0002-2179-2217" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "colorspace", "role": "Imports" }, { "package": "farver", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "colourpicker", "role": "Suggests" }, { "package": "shinyjs", "role": "Suggests" }, { "package": "dendextend", "role": "Suggests" } ], "_owner": "thisishcb", 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"https://github.com/thisishcb/palettome", "_realowner": "thisishcb", "_cranurl": true, "_releases": [ { "version": "1.0.1", "date": "2026-10-20" } ], "_exports": [ "as_cluster_data", "cluster_colors", "color_distance", "compute_centroids", "compute_family_dendrogram", "cut_families", "detect_families", "downsample_stratified", "export_palette_csv", "export_palette_json", "family_colors", "generate_palette", "import_palette_json", "launch_palettome_ui", "optimize_color", "plot_dendrogram", "plot_palette_static", "plot_swatches", "reset_overrides", "set_manual_color", "simulate_cvd" ], "_help": [ { "page": "as_cluster_data", "title": "Build a palettome data object from a data frame or Seurat object", "topics": [ "as_cluster_data", "as_cluster_data.data.frame", "as_cluster_data.Seurat" ] }, { "page": "cluster_colors", "title": "Get cluster colors as a named vector or a plain data frame", "topics": [ "cluster_colors" ] }, { "page": "color_distance", "title": "Pairwise perceptual color distance", "topics": [ "color_distance" ] }, { "page": "compute_centroids", "title": "Compute per-cluster centroids and cell counts", "topics": [ "compute_centroids" ] }, { "page": "compute_family_dendrogram", "title": "Build a cluster-distance dendrogram for family detection", "topics": [ "compute_family_dendrogram" ] }, { "page": "cut_families", "title": "Cut a precomputed dendrogram into families", "topics": [ "cut_families" ] }, { "page": "detect_families", "title": "Detect (or pass through) cluster families", "topics": [ "detect_families" ] }, { "page": "downsample_stratified", "title": "Stratified per-cluster subsample for interactive preview", "topics": [ "downsample_stratified" ] }, { "page": "export_palette_csv", "title": "Export cluster and/or family color tables as CSV", "topics": [ "export_palette_csv" ] }, { "page": "export_palette_json", "title": "Export a palette session to JSON", "topics": [ "export_palette_json" ] }, { "page": "family_colors", "title": "Get family colors as a named vector or a plain data frame", "topics": [ "family_colors" ] }, { "page": "generate_palette", "title": "Generate a cluster/family color palette", "topics": [ "generate_palette" ] }, { "page": "import_palette_json", "title": "Import a palette session from JSON", "topics": [ "import_palette_json" ] }, { "page": "launch_palettome_ui", "title": "Launch the interactive Palettome Shiny UI", "topics": [ "launch_palettome_ui" ] }, { "page": "optimize_color", "title": "Snap a hand-picked color into the palette's aesthetic envelope", "topics": [ "optimize_color" ] }, { "page": "plot_dendrogram", "title": "Plot a dendrogram preview of detected families", "topics": [ "plot_dendrogram" ] }, { "page": "plot_palette_static", "title": "Static plot of an embedding colored by the current palette", "topics": [ "plot_palette_static" ] }, { "page": "plot_swatches", "title": "Standalone swatch/legend figure, grouped by family", "topics": [ "plot_swatches" ] }, { "page": "reset_overrides", "title": "Reset manual color overrides", "topics": [ "reset_overrides" ] }, { "page": "set_manual_color", "title": "Manually set a cluster's or family's color", "topics": [ "set_manual_color" ] }, { "page": "simulate_cvd", "title": "Simulate color-vision deficiency on a palette", "topics": [ "simulate_cvd" ] } ], "_readme": "https://github.com/thisishcb/palettome/raw/HEAD/README.md", "_rundeps": [ "colorspace", "farver", "jsonlite" ], "_vignettes": [ { "source": "palettome.Rmd", "filename": "palettome.html", "title": "Getting started with palettome", "engine": "knitr::rmarkdown", "headings": [ "What this package is for", "Example data", "Step 1: build a palettome_data object", "The same step with a Seurat object", "Step 2: detect families", "Step 3: generate a palette", "Harmonious mode", "Contrast mode", "Steering the look", "Step 4: manual overrides", "Checking the palette", "Using the colors elsewhere", "Saving and resuming", "Large datasets", "The interactive UI" ], "created": 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