{
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  "Package": "gapmap",
  "Title": "Drawing Gapped Cluster Heatmaps with 'ggplot2'",
  "Version": "1.0.0",
  "Authors@R": "c(person(\"Ryo\", \"Sakai\", email=\"ryo@vda-lab.be\", role=\"aut\"), person(\"Evan\", \"Biederstedt\", email=\"evan.biederstedt@gmail.com\", role=c(\"cre\", \"aut\")))",
  "Description": "The gap encodes the distance between clusters and improves\ninterpretation of cluster heatmaps. The gaps can be of the same\ndistance based on a height threshold to cut the dendrogram.\nAnother option is to vary the size of gaps based on the\ndistance between clusters.",
  "License": "GPL-2 | GPL-3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/evanbiederstedt/gapmap",
  "BugReports": "https://github.com/evanbiederstedt/gapmap/issues",
  "RoxygenNote": "7.2.3",
  "NeedsCompilation": "no",
  "Maintainer": "Evan Biederstedt <evan.biederstedt@gmail.com>",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://evanbiederstedt.r-universe.dev",
  "Date/Publication": "2024-01-22 17:42:04 UTC",
  "RemoteUrl": "https://github.com/evanbiederstedt/gapmap",
  "RemoteRef": "HEAD",
  "RemoteSha": "e5664e487abd0032b4b5533cacb4cc18317b4eff",
  "Packaged": {
    "Date": "2026-06-14 08:09:12 UTC",
    "User": "root"
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  "Author": "Ryo Sakai [aut],\nEvan Biederstedt [cre, aut]",
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  "_user": "evanbiederstedt",
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    "message": "update v1.0.0\n",
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  "_devurl": "https://github.com/evanbiederstedt/gapmap",
  "_searchresults": 29,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/gapmap.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/evanbiederstedt/gapmap",
  "_realowner": "evanbiederstedt",
  "_cranurl": true,
  "_releases": [
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      "date": "2014-09-11"
    },
    {
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      "date": "2014-09-29"
    },
    {
      "version": "0.0.3",
      "date": "2015-11-16"
    },
    {
      "version": "0.0.4",
      "date": "2015-12-14"
    },
    {
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      "date": "2021-04-19"
    },
    {
      "version": "1.0.0",
      "date": "2024-01-22"
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    "assign_branch_positions",
    "assign_positions",
    "calculate_gap",
    "count_gap",
    "extract_list",
    "format_number",
    "gap_data",
    "gap_dendrogram",
    "gap_heatmap",
    "gap_label",
    "gapmap",
    "get_most_left_leaf",
    "get_most_right_leaf",
    "get_segment_df",
    "is.gapdata",
    "map",
    "map.exp",
    "set_most_right_leaf",
    "sum_distance"
  ],
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      "name": "sample_tcga",
      "title": "Sample data matrix from the integrated pathway analysis of gastric cancer from the Cancer Genome Atlas (TCGA) study.",
      "object": "sample_tcga",
      "file": "sample_tcga.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "percent_lymphocyte_infiltration",
        "tumor_nuclei_percent",
        "EBV.pos",
        "East.Asia",
        "percent_monocyte_infiltration",
        "year_of_initial_pathologic_diagnosis",
        "age_at_initial_pathologic_diagnosis",
        "RHOA.34_42",
        "RHOA.57_62",
        "MutSig2_rateTot_perMb",
        "MutSig_rateDbSnp_perMb",
        "Nonsilent.Mutation.Rate",
        "Silent.Mutation.Rate",
        "Total.Mutation.Rate",
        "absolute_extract_ploidy",
        "absolute_extract_purity",
        "days_to_birth",
        "percent_necrosis",
        "Number.of.Structural.Rearrangments.RNAseq",
        "MLH1_epigenetically_silenced",
        "diffuse_meth_subtype",
        "GEJUNC_CARDIA_EPC",
        "structural_rearrangement_count_WGS",
        "percent_neutrophil_infiltration",
        "M.EPC",
        "APC.code_potential_somatic",
        "ARID1A.code_potential_somatic",
        "BCOR.code_potential_somatic",
        "CDH1.code_potential_somatic",
        "CYP7B1.code_potential_somatic",
        "ERBB3.code_potential_somatic",
        "FMN2.code_potential_somatic",
        "GLI3.code_potential_somatic",
        "KCNMB2.code_potential_somatic",
        "KIAA2022.code_potential_somatic",
        "percent_normal_cells",
        "MUC17.code_potential_somatic",
        "NRK.code_potential_somatic",
        "PIK3CA.code_potential_somatic",
        "PTEN.code_potential_somatic",
        "RHOA.code_potential_somatic",
        "RNF43.code_potential_somatic",
        "SLCO1B3.code_potential_somatic",
        "TLR4.code_potential_somatic",
        "TP53.code_potential_somatic",
        "PIK3CA.E545K",
        "PIK3CA.H1047R",
        "MSI.H",
        "MSI.L",
        "MSS",
        "Canada",
        "Germany",
        "South.Korea",
        "Poland",
        "Russia",
        "Ukraine",
        "UNITED_STATES__country",
        "Vietnam",
        "FEMALE__gender",
        "MALE__gender",
        "ANTRUM__MAJOR_ANATOMIC_SITE_EPC",
        "FUNDUS_BODY__MAJOR_ANATOMIC_SITE_EPC",
        "GEJ_CARDIA__MAJOR_ANATOMIC_SITE_EPC",
        "Antrum.vs..all.other.anatomic.sites",
        "Antrum.pyloris.vs..all.other.anatomic.sites",
        "Body.vs..all.other.anatomic.sites",
        "Cardia.vs..all.other.anatomic.sites",
        "Fundus.vs..all.other.anatomic.sites",
        "Fundus.body.vs..all.other.anatomic.sites",
        "GE.junction.vs..all.other.anatomic.sites",
        "pathologic.M0.EPC",
        "M1__pathologic_M_epc",
        "N0__pathologic_N_epc",
        "N1__pathologic_N_epc",
        "N2__pathologic_N_epc",
        "N3__pathologic_N_epc",
        "GASTRIC.CIMP",
        "GASTRIC.EBV.CIMP",
        "Non.CIMP.DNA.Methylation",
        "EBV.KB.Subgroup",
        "MSI.H.KB.Subgroup",
        "SCNA.High.KB.Subgroup",
        "SCNA.Low.KB.Subgroup",
        "MicroRNA.Cluster.1",
        "MicroRNA.Cluster.2",
        "MicroRNA.Cluster.3",
        "MicroRNA.Cluster.4",
        "MicroRNA.Cluster.5",
        "TRUE__MLH1_methylation",
        "HIGH__SCNA_group",
        "LOW__SCNA_group",
        "Hypermutated",
        "Standard.Mutation.Rate",
        "Diffuse",
        "INTESTINAL__pathology_lauren",
        "Mixed.lauren",
        "EARLY__STAGE_EARLY_LATE",
        "LATE__STAGE_EARLY_LATE",
        "Stage.I.vs..all.other.stages",
        "Stage.II.vs..all.other.stages",
        "Stage.III.vs..all.other.stages",
        "Stage.IV.vs..all.other.stages",
        "ASIAN__race",
        "RPPA.Cluster.1",
        "RPPA.Cluster.2",
        "RPPA.Cluster.3",
        "Gene.Expression.Cluster.1",
        "Gene.Expression.Cluster.2",
        "Gene.Expression.Cluster.3",
        "Gene.Expression.Cluster.4",
        "Mucinous.vs..other.intestinal",
        "Papillary.vs..other.intestinal",
        "Tubular.vs..other.intestinal",
        "percent_stromal_cells",
        "percent_tumor_cells",
        "percent_tumor_nuclei",
        "tumor_necrosis_percent"
      ],
      "rows": 215,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "gapmap-package",
      "title": "Draws gapped heatmap (gapmap) and gapped dendrograms using ggplot2 in [R].",
      "topics": [
        "gapmap-package"
      ]
    },
    {
      "page": "gap_data",
      "title": "Generate a gapdata class object from a dendrogram object",
      "topics": [
        "gap_data"
      ]
    },
    {
      "page": "gap_dendrogram",
      "title": "Function to draw a gapped dendrogram",
      "topics": [
        "gap_dendrogram"
      ]
    },
    {
      "page": "gap_heatmap",
      "title": "Function to draw a gapped heatmap",
      "topics": [
        "gap_heatmap"
      ]
    },
    {
      "page": "gap_label",
      "title": "Function to draw a gapped labels",
      "topics": [
        "gap_label"
      ]
    },
    {
      "page": "gapmap",
      "title": "Function to draw a gapped cluster heatmap",
      "topics": [
        "gapmap"
      ]
    },
    {
      "page": "sample_tcga",
      "title": "Sample data matrix from the integrated pathway analysis of gastric cancer from the Cancer Genome Atlas (TCGA) study.",
      "topics": [
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      ]
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  "_nocasepkg": "gapmap",
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