# 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'