# spatialHeatmap

## Documentation for package ‘spatialHeatmap’ version 2.0.0

- 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
com_factor | Combine Factors in Targets File
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
edit_tar | Edit Targets Files
filter_data | Filter the Data Matrix
lis.deg.up.down | A nested list of differentialy-expressed genes (DEGs) detected by different methods
matrix_hm | Matrix Heatmap
network | Visualize a Target Assayed Item in a Network Graph
norm_data | Normalize Sequencing Count Matrix
profile_gene | Plot Gene Expression Profiles in a Data Frame
read_cache | Read R Objects from Cache
read_fr | Import Data from Tabular Files
read_hdf5 | Read Data from the Shiny App Database
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 | Create Spatial Heatmaps
submatrix | Subset Target Assayed Items and Their Nearest Neighbors
sub_data | Subset Target Data for Spatial Enrichment
update_feature | Update aSVG Spatial Features
write_hdf5 | Construct Database for the Shiny App