SPHM-class              The SPHM class
SPHMMethods             Methods for S4 class 'SPHM'
SVG-class               The SVG class for storing annotated SVG (aSVG)
                        instances
SVGMethods              Methods for S4 class 'SVG'
SpatialEnrichment       Identifying spatially enriched or depleted
                        biomolecules
aSVG.remote.repo        A list of URLs of remote aSVG repos
adj_mod                 Computing adjacency matrix and identifying
                        network modules
aggr_rep                Aggregate "Sample__Condition" Replicates in
                        Data Matrix
cell_group              Add manual cell group labels to
                        SingleCellExperiment
cluster_cell            Cluster single cells or combination of single
                        cells and bulk
coclus_opt              Optimization of co-clustering bulk and single
                        cell data
cocluster               Co-clustering bulk and single cell data
com_factor              Combine Factors in Targets File
covis                   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
data_ref                Calculating relative expression values
database                Creat databases for the Shiny App
edit_tar                Edit Targets Files
filter_data             Filtering the Data Matrix
matrix_hm               Hierarchical clustering combined with matrix
                        heatmap
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
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
optimal_k               Using the elbow method to find the optimal
                        number of clusters in K-means clustering
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
qc_cell                 Quality control in single cell data
read_cache              Read R Objects from Cache
read_fr                 Import Data from Tabular Files
read_svg                Parsing annotated SVG (aSVG) files
reduce_dim              Reducing dimensionality in count data
reduce_rep              Reduce sample replicates
return_feature          Return aSVG Files Relevant to Target Features
save_cache              Save R Objects in Cache
shiny_shm               Integrated Shiny App
shm                     Plot Spatial Heatmaps
spatialHeatmap-package
                        spatialHeatmap: Visualizing Spatial Assays in
                        Anatomical Images and Large-Scale Data
                        Extensions Spatial Heatmap, Spatial Enrichment,
                        Data Mining, Co-visualization
spatial_hm              Plot Spatial Heatmaps
submatrix               Subsetting data matrix
true_bulk               Assign true bulk to cells in 'colData' slot.
update_feature          Update aSVG Spatial Features
write_svg               Exporting each spatial heatmap to a separate
                        SVG file
