{"id":"https://openalex.org/W3190052239","doi":"https://doi.org/10.7490/f1000research.1118686.1","title":"spatialHeatmap: Visualizing spatial assays in anatomical images and network graphs","display_name":"spatialHeatmap: Visualizing spatial assays in anatomical images and network graphs","publication_year":2021,"publication_date":"2021-08-02","ids":{"openalex":"https://openalex.org/W3190052239","doi":"https://doi.org/10.7490/f1000research.1118686.1","mag":"3190052239"},"language":"en","primary_location":{"id":"doi:10.7490/f1000research.1118686.1","doi":"https://doi.org/10.7490/f1000research.1118686.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1118686.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"other","indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.7490/f1000research.1118686.1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100618158","display_name":"Jianhai Zhang","orcid":"https://orcid.org/0000-0002-0330-6908","observed_orcids":["https://orcid.org/0000-0002-0330-6908"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jianhai Zhang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073616037","display_name":"Jordan Hayes","orcid":"https://orcid.org/0000-0002-9983-9935","observed_orcids":["https://orcid.org/0000-0002-9983-9935"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jordan Hayes","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Le Zhang","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Le Zhang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086513946","display_name":"Bing Yang","orcid":"https://orcid.org/0000-0002-8978-2322","observed_orcids":["https://orcid.org/0000-0002-8978-2322"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bing Yang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078963967","display_name":"Wolf Bernd Frommer","orcid":"https://orcid.org/0000-0001-6465-0115","observed_orcids":["https://orcid.org/0000-0001-6465-0115","https://orcid.org/0000-0002-7622-1139"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wolf B Frommer","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001525551","display_name":"Julia N. Bailey-Serres","orcid":"https://orcid.org/0000-0002-8568-7125","observed_orcids":["https://orcid.org/0000-0002-8568-7125"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Julia Bailey-Serres","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5039923525","display_name":"Thomas Girke","orcid":"https://orcid.org/0000-0003-0710-3777","observed_orcids":["https://orcid.org/0000-0003-0710-3777"]},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thomas Girke","raw_affiliation_strings":["University of California, Riverside, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Riverside, USA","institution_ids":["https://openalex.org/I103635307"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5039923525"],"corresponding_institution_ids":["https://openalex.org/I103635307"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"10","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8628000020980835,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8628000020980835,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.05829999968409538,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.0364999994635582,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/spatial-data-visualization","display_name":"spatial data visualization","score":0.6959999799728394},{"id":"https://openalex.org/keywords/anatomical-images","display_name":"anatomical images","score":0.7620000243186951},{"id":"https://openalex.org/keywords/network-graphs","display_name":"network graphs","score":0.7770000100135803},{"id":"https://openalex.org/keywords/gene-modules","display_name":"gene modules","score":0.5569999814033508},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"hierarchical clustering","score":0.652999997138977},{"id":"https://openalex.org/keywords/tissue-specific-expression","display_name":"tissue-specific gene expression","score":0.8339999914169312},{"id":"https://openalex.org/keywords/shiny-app","display_name":"Shiny app","score":0.7620000243186951},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.8429999947547913}],"concepts":[{"id":"https://openalex.org/C2983643791","wikidata":"https://www.wikidata.org/wiki/Q1999993","display_name":"Open peer review","level":3,"score":0.8565610647201538},{"id":"https://openalex.org/C2992936677","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Plant biology","level":2,"score":0.7719817161560059},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.5254972577095032},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46358370780944824},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.450613409280777},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3450981676578522},{"id":"https://openalex.org/C42407357","wikidata":"https://www.wikidata.org/wiki/Q521","display_name":"Physiology","level":1,"score":0.3442949056625366},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33533957600593567},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.06821167469024658}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.7490/f1000research.1118686.1","doi":"https://doi.org/10.7490/f1000research.1118686.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1118686.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"doi:10.7490/f1000research.1118686.1","doi":"https://doi.org/10.7490/f1000research.1118686.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1118686.1","pdf_url":null,"source":{"id":"https://openalex.org/S7407050752","display_name":"Faculty of 1000 Research Ltd","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Other"},{"id":"mag:3190052239","doi":null,"is_oa":true,"landing_page_url":"https://f1000research.com/posters/10-724","pdf_url":null,"source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":"F1000Research","raw_type":null}],"best_oa_location":{"id":"doi:10.7490/f1000research.1118686.1","doi":"https://doi.org/10.7490/f1000research.1118686.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1118686.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391467917","https://openalex.org/W7025455052","https://openalex.org/W6958649032","https://openalex.org/W4410332212","https://openalex.org/W4401636196","https://openalex.org/W7158839072","https://openalex.org/W2762082538","https://openalex.org/W4411755159","https://openalex.org/W6963300105","https://openalex.org/W3134482219"],"abstract_inverted_index":{"The":[0,31,88,122],"spatialHeatmap":[1,125],"package":[2,51],"provides":[3,159],"functionalities":[4,123,223],"for":[5,65,220],"visualizing":[6],"cell-,":[7],"tissue-":[8],"and":[9,85,163,181],"organ-specific":[10],"data":[11,97],"of":[12,49,67,102,107,124,152,173],"biological":[13],"assays":[14],"by":[15,43,144],"coloring":[16],"the":[17,37,44,50,156,167,189],"corresponding":[18],"spatial":[19,55],"features":[20,175],"defined":[21],"in":[22,119,130],"anatomical":[23],"images":[24],"according":[25],"to":[26,35,92,161,179],"a":[27,54,131,138,145,171,216],"numeric":[28],"color":[29,32],"key.":[30],"scheme":[33],"used":[34,128,194],"represent":[36],"assay":[38,96],"values":[39],"can":[40,126,192,211],"be":[41,127,193,212],"customized":[42],"user.":[45],"This":[46],"core":[47],"functionality":[48],"is":[52,60,112,149],"called":[53],"heatmap":[56],"(SHM)":[57],"plot.":[58],"It":[59],"enhanced":[61],"with":[62,81,98,186,224],"visualization":[63],"tools":[64],"groups":[66],"measured":[68],"items":[69],"(e.g.":[70,205],"gene":[71],"modules)":[72],"sharing":[73],"related":[74],"abundance":[75,110],"profiles,":[76],"including":[77],"matrix":[78],"heatmaps":[79],"combined":[80],"hierarchical":[82],"clustering":[83],"dendrograms":[84],"network":[86],"representations.":[87],"environment":[89],"also":[90,113,150],"allows":[91],"co-visualize":[93],"single":[94],"cell":[95],"various":[99],"embedding":[100],"algorithms":[101],"high-dimensional":[103],"data.":[104,228],"Automated":[105],"detection":[106],"spatially":[108],"enriched":[109],"differences":[111],"supported,":[114],"such":[115],"as":[116,199,201,215],"genes":[117],"expressed":[118],"specific":[120],"tissues.":[121],"either":[129],"command-driven":[132],"mode":[133,158],"from":[134],"within":[135],"R":[136],"or":[137,207],"graphical":[139],"user":[140],"interface":[141],"(GUI)":[142],"provided":[143],"Shiny":[146,168,190],"App":[147,169,191],"that":[148,176,210],"part":[151],"this":[153],"package.":[154],"While":[155],"R-based":[157],"flexibility":[160],"customize":[162],"automate":[164],"analysis":[165],"routines,":[166],"includes":[170],"variety":[172],"convenience":[174],"will":[177],"appeal":[178],"experimentalists":[180],"other":[182],"users":[183],"less":[184],"familiar":[185],"R.":[187],"Moreover,":[188],"on":[195],"both":[196],"local":[197],"computers":[198],"well":[200],"centralized":[202],"server-based":[203],"deployments":[204],"cloud-based":[206],"custom":[208],"servers)":[209],"accessed":[213],"remotely":[214],"public":[217],"web":[218],"service":[219],"using":[221],"spatialHeatmap's":[222],"community":[225],"and/or":[226],"private":[227]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2021-08-16T00:00:00"}
