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

## Documentation for package ‘spatialHeatmap’ version 2.12.1

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

## Help Pages

A B C D E F G L M N O P Q R S T U W misc

spatialHeatmap-package | spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions Spatial Heatmap, Spatial Enrichment, Data Mining, Co-visualization

## -- A --

adj_mod | Computing adjacency matrix and identifying network modules
aggr_rep | Aggregate "Sample__Condition" Replicates in Data Matrix
angle | Methods for S4 class 'SVG'
angle-method | Methods for S4 class 'SVG'
angle<- | Methods for S4 class 'SVG'
angle<--method | Methods for S4 class 'SVG'
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'

## -- B --

bulk | Methods for S4 class 'SPHM'
bulk-method | Methods for S4 class 'SPHM'
bulk<- | Methods for S4 class 'SPHM'
bulk<--method | Methods for S4 class 'SPHM'

## -- C --

cell | Methods for S4 class 'SPHM'
cell-method | Methods for S4 class 'SPHM'
cell<- | Methods for S4 class 'SPHM'
cell<--method | Methods for S4 class 'SPHM'
cell_group | Add manual cell group labels to SingleCellExperiment
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 spatialHeatmap Shiny Apps
cut_dendro | Cutting dendrograms
cvt_id | Converting gene ids using annotation databases

## -- D --

database | Creat databases for the Shiny App
data_ref | Calculating relative expression values
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'

## -- E --

edit_tar | Edit Targets Files

## -- F --

filter_asg | Co-clustering bulk and single cell data
filter_cell | Co-clustering bulk and single cell data
filter_data | Filtering the Data Matrix

## -- G --

graph_line | Identifying spatially enriched or depleted biomolecules

## -- L --

length | Methods for S4 class 'SPHM'
length-method | Methods for S4 class 'SPHM'
length-method | Methods for S4 class 'SVG'

## -- M --

match | Methods for S4 class 'SPHM'
match-method | Methods for S4 class 'SPHM'
match<- | Methods for S4 class 'SPHM'
match<--method | Methods for S4 class 'SPHM'
matrix_hm | Hierarchical clustering combined with matrix heatmap

## -- N --

name | Methods for S4 class 'SPHM'
name-method | Methods for S4 class 'SPHM'
names | Methods for S4 class 'SVG'
names-method | Methods for S4 class 'SVG'
names<--method | Methods for S4 class 'SVG'
network | Network graphs
norm_cell | Normalizing single cell data
norm_data | Normalize Sequencing Count Matrix
norm_srsc | Jointl normalization of spatially resolved single cell data and bulk data

## -- O --

optimal_k | Using the elbow method to find the optimal number of clusters in K-means clustering
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
output | Methods for S4 class 'SPHM'
output-method | Methods for S4 class 'SPHM'
output<- | Methods for S4 class 'SPHM'
output<--method | Methods for S4 class 'SPHM'
ovl_enrich | Identifying spatially enriched or depleted biomolecules

## -- P --

plot_dim | Embedding plots of single cells/bulk tissues after co-clustering
plot_kmeans | Plotting the clusters returned by K-means clustering
plot_meta | Meta function for plotting spatial heatmaps or co-visualizing bulk and single cell data
process_cell_meta | Processing single cell RNA-seq count data

## -- Q --

qc_cell | Quality control in single cell data
query_enrich | Identifying spatially enriched or depleted biomolecules

## -- R --

raster_pa | Methods for S4 class 'SVG'
raster_pa-method | Methods for S4 class 'SVG'
raster_pa<- | Methods for S4 class 'SVG'
raster_pa<--method | Methods for S4 class 'SVG'
read_cache | Read R Objects from Cache
read_fr | Import Data from Tabular Files
read_hdf5 | Creat databases for the Shiny App
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
return_feature | Return aSVG Files Relevant to Target Features

## -- S --

save_cache | Save R Objects in Cache
sf_var | Identifying spatially enriched or depleted biomolecules
shiny_shm | Integrated Shiny App
shm | Plot Spatial Heatmaps
shm-method | Plot Spatial Heatmaps
SpatialEnrichment | Identifying spatially enriched or depleted biomolecules
spatialHeatmap | spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions Spatial Heatmap, Spatial Enrichment, Data Mining, Co-visualization
spatial_enrich | Identifying spatially enriched or depleted biomolecules
spatial_hm | Plot Spatial Heatmaps
spatial_hm-method | Plot Spatial Heatmaps
SPHM | The SPHM class
SPHM-class | The SPHM class
SPHMMethods | Methods for S4 class 'SPHM'
submatrix | Subsetting data matrix
sub_sf | Methods for S4 class 'SVG'
sub_sf-method | Methods for S4 class 'SVG'
SVG | The SVG class for storing annotated SVG (aSVG) instances
svg | Methods for S4 class 'SPHM'
SVG-class | The SVG class for storing annotated SVG (aSVG) instances
svg-method | Methods for S4 class 'SPHM'
svg<- | Methods for S4 class 'SPHM'
svg<--method | Methods for S4 class 'SPHM'
SVGMethods | Methods for S4 class 'SVG'
svg_obj | Methods for S4 class 'SVG'
svg_obj-method | Methods for S4 class 'SVG'
svg_obj<- | Methods for S4 class 'SVG'
svg_obj<--method | Methods for S4 class 'SVG'

## -- T --

true_bulk | Assign true bulk to cells in 'colData' slot.

## -- U --

update_feature | Update aSVG Spatial Features

## -- W --

write_hdf5 | Creat databases for the Shiny App
write_svg | Exporting each spatial heatmap to a separate SVG file

## -- misc --

[-method | Methods for S4 class 'SPHM'
[-method | Methods for S4 class 'SVG'
[<--method | Methods for S4 class 'SPHM'
[<--method | Methods for S4 class 'SVG'