spatialHeatmap

---

Documentation for package ‘spatialHeatmap’ version 2.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

spatialHeatmap-package	spatialHeatmap Spatial Heatmap, Matrix Heatmap, Network
adj_mod	Compute Adjacency Matrix and Identify Modules
aggr_rep	Aggregate "Sample__Condition" Replicates in Data Matrix
aSVG.remote.repo	A list of URLs of remote aSVG repos
attribute	Methods for S4 class 'SVG'
attribute-method	Methods for S4 class 'SVG'
attribute<-	Methods for S4 class 'SVG'
attribute<--method	Methods for S4 class 'SVG'
cluster_cell	Cluster single cells or combination of single cells and bulk
cmb	Methods for S4 class 'SVG'
cmb-method	Methods for S4 class 'SVG'
cocluster	Co-clustering bulk and single cell data
coclus_opt	Optimization of co-clustering bulk and single cell data
com_factor	Combine Factors in Targets File
coordinate	Methods for S4 class 'SVG'
coordinate-method	Methods for S4 class 'SVG'
coordinate<-	Methods for S4 class 'SVG'
coordinate<--method	Methods for S4 class 'SVG'
covis	Co-visualizing spatial heatmaps with single cell embedding plots
covis-method	Co-visualizing spatial heatmaps with single cell embedding plots
custom_shiny	Create Customized Shiny App of Spaital Heatmap
deg.table	A table of differentialy-expressed genes (DEGs) detected by different methods
deg_ovl	Plot Overlap of Spatially-Enriched Genes Across Methods
desired_bulk_shiny	Co-clustering bulk and single cell data
dimension	Methods for S4 class 'SVG'
dimension-method	Methods for S4 class 'SVG'
dimension<-	Methods for S4 class 'SVG'
dimension<--method	Methods for S4 class 'SVG'
edit_tar	Edit Targets Files
filter_asg	Co-clustering bulk and single cell data
filter_cell	Co-clustering bulk and single cell data
filter_data	Filter the Data Matrix
graph_line	Plot Gene Expression Profiles in a Data Frame
length-method	Methods for S4 class 'SVG'
lis.deg.up.down	A nested list of differentialy-expressed genes (DEGs) detected by different methods
manual_group	Add manual cell group labels to SingleCellExperiment
matrix_hm	Matrix Heatmap
names	Methods for S4 class 'SVG'
names-method	Methods for S4 class 'SVG'
names<--method	Methods for S4 class 'SVG'
network	Visualize a Target Assayed Item in a Network Graph
norm_cell	Normalizing single cell data
norm_data	Normalize Sequencing Count Matrix
opt_bar	Bar plots of co-clustering optimization results.
opt_setting	Bar plots of co-clustering optimization results.
opt_violin	Violin plots of co-clustering validation results
plot_dim	Embedding plots of single cells/bulk tissues after co-clustering
process_cell_meta	Processing single cell RNA-seq count data
qc_cell	Quality control in single cell data
raster	Methods for S4 class 'SVG'
raster-method	Methods for S4 class 'SVG'
raster<-	Methods for S4 class 'SVG'
raster<--method	Methods for S4 class 'SVG'
read_cache	Read R Objects from Cache
read_fr	Import Data from Tabular Files
read_hdf5	Read Data from the Shiny App Database
read_svg	Parsing annotated SVG (aSVG) files
reduce_dim	Reducing dimensionality in count data
reduce_rep	Reduce sample replicates
refine_asg	Co-clustering bulk and single cell data
refine_cluster	Refine single cell clusters
return_feature	Return aSVG Files Relevant to Target Features
save_cache	Save R Objects in Cache
shiny_shm	Integrated Shiny App
spatialHeatmap	spatialHeatmap Spatial Heatmap, Matrix Heatmap, Network
spatial_enrich	Identify Spatial Feature-Specifcally Expressed Genes
spatial_hm	Plot Spatial Heatmaps
spatial_hm-method	Plot Spatial Heatmaps
submatrix	Subset Target Assayed Items and Their Nearest Neighbors
sub_ft	Methods for S4 class 'SVG'
sub_ft-method	Methods for S4 class 'SVG'
SVG	The SVG class for storing annotated SVG (aSVG) instances
svg	Methods for S4 class 'SVG'
SVG-class	The SVG class for storing annotated SVG (aSVG) instances
svg-method	Methods for S4 class 'SVG'
svg<-	Methods for S4 class 'SVG'
svg<--method	Methods for S4 class 'SVG'
SVGMethods	Methods for S4 class 'SVG'
tar_ref	Subset Target Data for Spatial Enrichment
true_bulk	Assign true bulk to cells in 'colData' slot.
update_feature	Update aSVG Spatial Features
write_hdf5	Construct Database for the Shiny App
[-method	Methods for S4 class 'SVG'
[<--method	Methods for S4 class 'SVG'