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"Title": "Data Visualisation on 'Lifemap' Tree",
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"Description": "Allow to visualise data on the NCBI phylogenetic tree as\npresented in Lifemap . It takes as\ninput a dataframe with at least a \"taxid\" column containing\nNCBI format TaxIds and allows to draw multiple layers with\ndifferent visualisation tools.",
"License": "MIT + file LICENSE",
"Encoding": "UTF-8",
"Roxygen": "list(markdown = TRUE)",
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"VignetteBuilder": "knitr",
"URL": "https://lifemap-tol.github.io/LifemapR/,\nhttps://github.com/Lifemap-ToL/LifemapR",
"BugReports": "https://github.com/Lifemap-ToL/LifemapR/issues",
"Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libicu-dev libpng-dev libuv1-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev zlib1g-dev",
"Repository": "https://lifemap-tol.r-universe.dev",
"Date/Publication": "2025-08-27 09:11:58 UTC",
"RemoteUrl": "https://github.com/lifemap-tol/lifemapr",
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"User": "root"
},
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},
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],
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"date": "2023-08-24"
},
{
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"date": "2024-03-20"
},
{
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"date": "2025-03-06"
},
{
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"date": "2025-08-27"
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],
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"create_matrix",
"display_map",
"draw_Lifemap",
"is.lifemap_obj",
"is.lm_branches",
"is.lm_markers",
"is.lm_piecharts",
"lifemap",
"lm_branches",
"lm_markers",
"lm_piecharts",
"make_newick",
"pass_infos",
"pass_infos_discret"
],
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"object": "eukaryotes_1000",
"file": "eukaryotes_1000.RData",
"class": [
"data.frame"
],
"fields": [
"X.Organism.Name",
"taxid",
"BioProject.Accession",
"BioProject.ID",
"Group",
"SubGroup",
"Size..Mb.",
"GC.",
"Assembly.Accession",
"Replicons",
"WGS",
"Scaffolds",
"Genes",
"Proteins",
"Release.Date",
"Modify.Date",
"Status",
"Center",
"BioSample.Accession"
],
"rows": 1000,
"table": true,
"tojson": true
},
{
"name": "eukaryotes_80",
"title": "NCBI information for 80 eukaryotes",
"object": "eukaryotes_80",
"file": "eukaryotes_80.RData",
"class": [
"data.frame"
],
"fields": [
"X.Organism.Name",
"taxid",
"BioProject.Accession",
"BioProject.ID",
"Group",
"SubGroup",
"Size..Mb.",
"GC.",
"Assembly.Accession",
"Replicons",
"WGS",
"Scaffolds",
"Genes",
"Proteins",
"Release.Date",
"Modify.Date",
"Status",
"Center",
"BioSample.Accession"
],
"rows": 80,
"table": true,
"tojson": true
},
{
"name": "gen_res",
"title": "Genomic results",
"object": "gen_res",
"file": "gen_res.RData",
"class": [
"data.frame"
],
"fields": [
"taxid",
"Genome_size",
"TEcontent_bp"
],
"rows": 808,
"table": true,
"tojson": true
},
{
"name": "kraken_res",
"title": "Kraken results",
"object": "kraken_res",
"file": "kraken_res.RData",
"class": [
"data.frame"
],
"fields": [
"coverage_percent",
"coverage_number",
"fragment_number",
"rank",
"taxid",
"name"
],
"rows": 4427,
"table": true,
"tojson": true
},
{
"name": "LM_eukaryotes",
"title": "Transformation in a LifemapR format of NCBI information for 1000 eukaryotes",
"object": "LM_eukaryotes",
"file": "LM_eukaryotes.RData",
"class": [
"lifemap_obj",
"list"
],
"fields": [],
"table": false,
"tojson": true
}
],
"_help": [
{
"page": "plus-.lifemap_obj",
"title": "Add a graphical element to a tree visualisation.",
"topics": [
"+.lifemap_obj"
]
},
{
"page": "add_lm_branches",
"title": "Compute the aesthetics for a subtree visualisation.",
"topics": [
"add_lm_branches"
]
},
{
"page": "add_lm_markers",
"title": "Compute the aesthetics for markers visualisation.",
"topics": [
"add_lm_markers"
]
},
{
"page": "add_lm_piecharts",
"title": "Compute the aesthetics for discret values visualisation.",
"topics": [
"add_lm_piecharts"
]
},
{
"page": "build_Lifemap",
"title": "A function to construct a LifemapR object, usable by the other functions of the package.",
"topics": [
"build_Lifemap"
]
},
{
"page": "create_matrix",
"title": "Create a dataframe for the ancestry.",
"topics": [
"create_matrix"
]
},
{
"page": "create_value_range",
"title": "Compute a new scale for a value",
"topics": [
"create_value_range"
]
},
{
"page": "display_map",
"title": "Create a Lifemap base.",
"topics": [
"display_map"
]
},
{
"page": "display_option",
"title": "Compute the different display options.",
"topics": [
"display_option"
]
},
{
"page": "draw_Lifemap",
"title": "Represent data on a Lifemap basemap.",
"topics": [
"draw_Lifemap"
]
},
{
"page": "eukaryotes_1000",
"title": "NCBI information for 1000 eukaryotes",
"topics": [
"eukaryotes_1000"
]
},
{
"page": "eukaryotes_80",
"title": "NCBI information for 80 eukaryotes",
"topics": [
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]
},
{
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"title": "Genomic results",
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]
},
{
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"topics": [
"is.lifemap_obj"
]
},
{
"page": "is.lm_branches",
"title": "Reports whether x is a lm_branches object.",
"topics": [
"is.lm_branches"
]
},
{
"page": "is.lm_markers",
"title": "Reports whether x is a lm_markers object.",
"topics": [
"is.lm_markers"
]
},
{
"page": "is.lm_piecharts",
"title": "Reports whether x is a lm_branches object.",
"topics": [
"is.lm_piecharts"
]
},
{
"page": "kraken_res",
"title": "Kraken results",
"topics": [
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]
},
{
"page": "lifemap",
"title": "Initialise a new Lifemap visualisation.",
"topics": [
"lifemap"
]
},
{
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"title": "Add a \"branches\" layer to a lifemap_obj object.",
"topics": [
"lm_branches"
]
},
{
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"title": "Transformation in a LifemapR format of NCBI information for 1000 eukaryotes",
"topics": [
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]
},
{
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"title": "add a \"markers\" layer to a lifemap_obj object.",
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"lm_markers"
]
},
{
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"title": "Add a \"piecharts\" layer to a lifemap_obj object.",
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]
},
{
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"title": "Create a newick for the given dataset.",
"topics": [
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]
},
{
"page": "pass_infos",
"title": "Infer numerical values to nodes.",
"topics": [
"pass_infos"
]
},
{
"page": "pass_infos_discret",
"title": "Infer discret values to nodes for lm_piecharts function.",
"topics": [
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]
},
{
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"title": "Method to print lifemap_obj objects.",
"topics": [
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}
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