Package: spatialHeatmap 2.11.0

Jianhai Zhang

spatialHeatmap: spatialHeatmap

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.

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_2.11.0.tar.gz
spatialHeatmap_2.11.0.zip(r-4.5)spatialHeatmap_2.11.0.zip(r-4.4)spatialHeatmap_2.11.0.zip(r-4.3)
spatialHeatmap_2.11.0.tgz(r-4.4-any)spatialHeatmap_2.11.0.tgz(r-4.3-any)
spatialHeatmap_2.11.0.tar.gz(r-4.5-noble)spatialHeatmap_2.11.0.tar.gz(r-4.4-noble)
spatialHeatmap_2.11.0.tgz(r-4.4-emscripten)spatialHeatmap_2.11.0.tgz(r-4.3-emscripten)
spatialHeatmap.pdf |spatialHeatmap.html✨
spatialHeatmap/json (API)
NEWS

# 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:

aSVG.remote.repo - A list of URLs of remote aSVG repos

On BioConductor:spatialHeatmap-2.11.0(bioc 3.20)spatialHeatmap-2.10.1(bioc 3.19)

bioconductor-package

80 exports 1.38 score 163 dependencies

Last updated 2 months agofrom:59099722a3

Exports:adj_mod aggr_rep angle angle<-attribute attribute<-bulk bulk<-cell cell_group cell<-cluster_cell cmb coclus_opt cocluster com_factor coordinate coordinate<-covis custom_shiny cut_dendro cvt_id data_ref desired_bulk_shiny dimension dimension<-edit_tar filter_asg filter_cell filter_data graph_line match match<-matrix_hm name network norm_cell norm_data norm_srsc opt_bar opt_setting opt_violin optimal_k output output<-ovl_enrich plot_dim plot_kmeans plot_meta process_cell_meta qc_cell query_enrich raster_pa raster_pa<-read_cache read_fr read_hdf5 read_svg reduce_dim reduce_rep refine_asg return_feature save_cache sf_var shiny_shm shm spatial_enrich spatial_hm SPHM sub_sf submatrix svg SVG svg_obj svg_obj<-svg<-true_bulk update_feature write_hdf5 write_svg

Dependencies:abind annotate AnnotationDbi askpass assertthat base64enc beachmat beeswarm BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bitops blob bluster bslib cachem Cairo caTools cli cluster codetools colorspace commonmark cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest dplyr dqrng edgeR fansi farver fastmap FNN fontawesome formatR fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggplot2 ggplotify ggrastr ggrepel glue gplots gridExtra gridGraphics grImport gtable gtools htmltools httpuv httr igraph IRanges irlba isoband jquerylib jsonlite KEGGREST KernSmooth labeling lambda.r later lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mgcv mime munsell nlme openssl pheatmap pillar pkgconfig plogr plyr png promises R6 ragg rappdirs RColorBrewer Rcpp RcppAnnoy RcppEigen RcppHNSW RcppML RcppProgress reshape2 rlang RSpectra RSQLite rsvd rsvg Rtsne S4Arrays S4Vectors sass ScaledMatrix scales scater scran scuttle shiny shinyAce shinydashboard shinytoastr SingleCellExperiment sitmo snow sourcetools SparseArray sparseMatrixStats spsComps statmod stringi stringr SummarizedExperiment survival sys systemfonts textshaping tibble tidyselect UCSC.utils utf8 uwot vctrs vipor viridis viridisLite withr XML xml2 xtable XVector yulab.utils zlibbioc

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

Authors: Jianhai Zhang and Thomas Girke

Rendered fromspatialHeatmap.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2024-04-19
Started: 2020-10-21

spatialHeatmap: Co-visualizing Bulk and Single-cell Assay Data

Authors: Jianhai Zhang and Thomas Girke

Rendered fromcovisualize.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2024-02-11
Started: 2022-06-09

Creating Custom Annotated SVGs

Authors: Jianhai Zhang

Rendered fromcustom_SVGs.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2024-02-11
Started: 2023-12-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
spatialHeatmap Spatial Heatmap, Spatial Enrichment, Data Mining, Co-visualization	spatialHeatmap-package spatialHeatmap
Computing adjacency matrix and identifying network modules	adj_mod
Aggregate "Sample__Condition" Replicates in Data Matrix	aggr_rep
A list of URLs of remote aSVG repos	aSVG.remote.repo
Add manual cell group labels to SingleCellExperiment	cell_group
Cluster single cells or combination of single cells and bulk	cluster_cell
Optimization of co-clustering bulk and single cell data	coclus_opt
Co-clustering bulk and single cell data	cocluster desired_bulk_shiny filter_asg filter_cell refine_asg
Combine Factors in Targets File	com_factor
Co-visualizing spatial heatmaps with single-cell embedding plots	covis covis,SPHM-method
Create Customized spatialHeatmap Shiny Apps	custom_shiny
Cutting dendrograms	cut_dendro
Converting gene ids using annotation databases	cvt_id
Calculating relative expression values	data_ref
Creat databases for the Shiny App	Database read_hdf5 write_hdf5
Edit Targets Files	edit_tar
Filtering the Data Matrix	filter_data
Hierarchical clustering combined with matrix heatmap	matrix_hm
Network graphs	network
Normalizing single cell data	norm_cell
Normalize Sequencing Count Matrix	norm_data
Jointl normalization of spatially resolved single cell data and bulk data	norm_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 results	opt_violin
Using the elbow method to find the optimal number of clusters in K-means clustering	optimal_k
Embedding plots of single cells/bulk tissues after co-clustering	plot_dim
Plotting the clusters returned by K-means clustering	plot_kmeans
Meta function for plotting spatial heatmaps or co-visualizing bulk and single cell data	plot_meta
Processing single cell RNA-seq count data	process_cell_meta
Quality control in single cell data	qc_cell
Read R Objects from Cache	read_cache
Import Data from Tabular Files	read_fr
Parsing annotated SVG (aSVG) files	read_svg
Reducing dimensionality in count data	reduce_dim
Reduce sample replicates	reduce_rep
Return aSVG Files Relevant to Target Features	return_feature
Save R Objects in Cache	save_cache
Integrated Shiny App	shiny_shm
Plot Spatial Heatmaps	shm shm,SPHM-method
Plot Spatial Heatmaps	spatial_hm spatial_hm,SVG-method
Identifying spatially enriched or depleted biomolecules	graph_line ovl_enrich query_enrich sf_var SpatialEnrichment spatial_enrich
The SPHM class	SPHM 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 matrix	submatrix
The SVG class for storing annotated SVG (aSVG) instances	SVG 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 Features	update_feature
Exporting each spatial heatmap to a separate SVG file	write_svg