Package: spatialHeatmap 2.19.2

Jianhai Zhang

spatialHeatmap: spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data. A description of the project is available here: https://spatialheatmap.org.

Authors:Jianhai Zhang [aut, trl, cre], Le Zhang [aut], Jordan Hayes [aut], Brendan Gongol [aut], Alexander Borowsky [aut], Julia Bailey-Serres [aut], Thomas Girke [aut]

spatialHeatmap_2.19.2.tar.gz
spatialHeatmap_2.19.2.zip(r-4.7-any)spatialHeatmap_2.19.2.zip(r-4.6-any)spatialHeatmap_2.19.2.zip(r-4.5-any)
spatialHeatmap_2.19.2.tgz(r-4.6-any)spatialHeatmap_2.19.2.tgz(r-4.5-any)
spatialHeatmap_2.19.2.tar.gz(r-4.7-any)spatialHeatmap_2.19.2.tar.gz(r-4.6-any)
spatialHeatmap_2.19.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spatialHeatmap/json (API)

# Install 'spatialHeatmap' in R:
install.packages('spatialHeatmap', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jianhaizhang/spatialheatmap/issues

Datasets:

On BioConductor:spatialHeatmap-2.19.2(bioc 3.24)spatialHeatmap-2.18.2(bioc 3.23)

spatialvisualizationmicroarraysequencinggeneexpressiondatarepresentationnetworkclusteringgraphandnetworkcellbasedassaysatacseqdnaseqtissuemicroarraysinglecellcellbiologygenetarget

6.58 score 7 stars 18 scripts 504 downloads 80 exports 107 dependencies

Last updated from:9b077b1ab0. Checks:6 ERROR, 4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR337
linux-develOK640
source / vignettesOK683
linux-releaseOK576
macos-releaseERROR373
macos-oldrelERROR409
windows-develERROR422
windows-releaseERROR428
windows-oldrelERROR423
wasm-releaseOK298

Exports:adj_modaggr_repangleangle<-attributeattribute<-bulkbulk<-cellcell_groupcell<-cluster_cellcmbcoclus_optcoclustercom_factorcoordinatecoordinate<-coviscustom_shinycut_dendrocvt_iddata_refdesired_bulk_shinydimensiondimension<-edit_tarfilter_asgfilter_cellfilter_datagraph_linematchmatch<-matrix_hmnamenetworknorm_cellnorm_datanorm_srscopt_baropt_settingopt_violinoptimal_koutputoutput<-ovl_enrichplot_dimplot_kmeansplot_metaprocess_cell_metaqc_cellquery_enrichraster_paraster_pa<-read_cacheread_frread_hdf5read_svgreduce_dimreduce_reprefine_asgreturn_featuresave_cachesf_varshiny_shmshmspatial_enrichspatial_hmSPHMsub_sfsubmatrixsvgSVGsvg_objsvg_obj<-svg<-true_bulkupdate_featurewrite_hdf5write_svg

Dependencies:abindannotateAnnotationDbiaskpassassertthatbase64encBiobaseBiocBaseUtilsBiocGenericsBiostringsbitbit64blobbslibcachemclicommonmarkcpp11crayoncurldata.tableDBIDelayedArraydigestdplyredgeRfarverfastmapfontawesomefsgenefiltergenericsGenomicRangesggplot2ggplotifygluegridExtragridGraphicsgrImportgtablehtmltoolshttpuvhttrigraphIRangesisobandjquerylibjsonliteKEGGRESTlabelinglaterlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigplyrpngpromisesR6rappdirsRColorBrewerRcppreshape2rlangRSQLitersvgS4ArraysS4VectorsS7sassscalesSeqinfoshinyshinyAceshinydashboardshinytoastrSingleCellExperimentsourcetoolsSparseArrayspsCompsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyselectutf8vctrsviridisLitewithrXMLxml2xtableXVectoryulab.utils

spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
Introduction | Motivation | Design | Image Format: SVG | Data Repositories | Tutorial Overview | Getting Started | Installation | Packages and Documentation | Spatial Heatmaps | Quick Start | aSVG Image | Numeric Data | Plot SHM | Human Brain | Gene Expression Data | aSVG Image | Experimental Design | Preprocess Assay Data | SHM: Multiple Genes | SHM: Other Selected Features | SHM: Customization | Mouse Organs | SHM: Transparency | Arabidopsis Shoot | SHM: Microarray | Superimposing raster and vector graphics | SHMs of Multiple Variables | SHM: Multiple Variables | Extended functionalities | Spatial Enrichment | Hierarchical Clustering | Network Graphs | Module Identification | Module Visualization | Shiny App | Local System | Server Deployment | Custom Shiny App | Database Backend | Supplementary Section | Numeric Data | Object Types | vector | data.frame | SummarizedExperiment | Advanced Functionalities | SHM: Re-matching | SHM: Time Series | Version Informaion | Funding | References
Rendered fromspatialHeatmap.Rmdusingknitr::rmarkdown

Last update: 2026-05-06
Started: 2020-10-21

spatialHeatmap: Co-visualizing Bulk and Single-cell Assay Data
Introduction | Overview | Data Structures | Getting Started | Installation | Packages and Documentation | Quick Start | Co-clustering Labels | Pre-processing | Co-clustering | Co-visualization | Spatial Single-Cell Data | Shiny App | Supplementary Section | Single-cell Clustering Labels | Co-clustering Labels: Other Coloring | Cell-by-Group | Feature-by-Group | Fixed-by-Group | Tailoring Co-clustering Results | Command-line Method | Graphical Method | Version Informaion | Funding | References
Rendered fromcovisualize.Rmdusingknitr::rmarkdown

Last update: 2026-05-06
Started: 2022-06-09

Creating Custom Annotated SVGs
Summary | Funding | References
Rendered fromcustom_SVGs.Rmdusingknitr::rmarkdown

Last update: 2026-05-06
Started: 2023-12-06

Readme and manuals

Help Manual

Help pageTopics
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions Spatial Heatmap, Spatial Enrichment, Data Mining, Co-visualizationspatialHeatmap-package spatialHeatmap
Computing adjacency matrix and identifying network modulesadj_mod
Aggregate "Sample__Condition" Replicates in Data Matrixaggr_rep
A list of URLs of remote aSVG reposaSVG.remote.repo
Add manual cell group labels to SingleCellExperimentcell_group
Cluster single cells or combination of single cells and bulkcluster_cell
Optimization of co-clustering bulk and single cell datacoclus_opt
Co-clustering bulk and single cell datacocluster desired_bulk_shiny filter_asg filter_cell refine_asg
Combine Factors in Targets Filecom_factor
Co-visualizing spatial heatmaps with single-cell embedding plotscovis covis,SPHM-method
Create Customized spatialHeatmap Shiny Appscustom_shiny
Cutting dendrogramscut_dendro
Converting gene ids using annotation databasescvt_id
Calculating relative expression valuesdata_ref
Creat databases for the Shiny Appdatabase read_hdf5 write_hdf5
Edit Targets Filesedit_tar
Filtering the Data Matrixfilter_data
Hierarchical clustering combined with matrix heatmapmatrix_hm
Network graphsnetwork
Normalizing single cell datanorm_cell
Normalize Sequencing Count Matrixnorm_data
Jointly normalization of spatially resolved single cell data and bulk datanorm_srsc
Bar plots of co-clustering optimization results.opt_bar
Bar plots of co-clustering optimization results.opt_setting
Violin plots of co-clustering validation resultsopt_violin
Using the elbow method to find the optimal number of clusters in K-means clusteringoptimal_k
Embedding plots of single cells/bulk tissues after co-clusteringplot_dim
Plotting the clusters returned by K-means clusteringplot_kmeans
Meta function for plotting spatial heatmaps or co-visualizing bulk and single cell dataplot_meta
Processing single cell RNA-seq count dataprocess_cell_meta
Quality control in single cell dataqc_cell
Read R Objects from Cacheread_cache
Import Data from Tabular Filesread_fr
Parsing annotated SVG (aSVG) filesread_svg
Reducing dimensionality in count datareduce_dim
Reduce sample replicatesreduce_rep
Return aSVG Files Relevant to Target Featuresreturn_feature
Save R Objects in Cachesave_cache
Integrated Shiny Appshiny_shm
Plot Spatial Heatmapsshm shm,SPHM-method
Plot Spatial Heatmapsspatial_hm spatial_hm,SVG-method
Identifying spatially enriched or depleted biomoleculesgraph_line ovl_enrich query_enrich sf_var SpatialEnrichment spatial_enrich
The SPHM classSPHM SPHM-class
Methods for S4 class 'SPHM'bulk bulk,SPHM-method bulk<- bulk<-,SPHM-method cell cell,SPHM-method cell<- cell<-,SPHM-method length length,SPHM-method match match,SPHM-method match<- match<-,SPHM-method name name,SPHM-method output output,SPHM-method output<- output<-,SPHM-method SPHMMethods svg svg,SPHM-method svg<- svg<-,SPHM-method [,SPHM,ANY,ANY,ANY-method [<-,SPHM,ANY,ANY,ANY-method
Subsetting data matrixsubmatrix
The SVG class for storing annotated SVG (aSVG) instancesSVG SVG-class
Methods for S4 class 'SVG'angle angle,SVG-method angle<- angle<-,SVG-method attribute attribute,SVG-method attribute<- attribute<-,SVG-method cmb cmb,SVG,SVG-method coordinate coordinate,SVG-method coordinate<- coordinate<-,SVG-method dimension dimension,SVG-method dimension<- dimension<-,SVG-method length,SVG-method names names,SVG-method names<-,SVG-method raster_pa raster_pa,SVG-method raster_pa<- raster_pa<-,SVG-method sub_sf sub_sf,SVG-method SVGMethods svg_obj svg_obj,SVG-method svg_obj<- svg_obj<-,SVG-method [,SVG,ANY,ANY,ANY-method [<-,SVG,ANY,ANY,ANY-method
Assign true bulk to cells in 'colData' slot.true_bulk
Update aSVG Spatial Featuresupdate_feature
Exporting each spatial heatmap to a separate SVG filewrite_svg