spatialHeatmap

---

Documentation for package ‘spatialHeatmap’ version 2.2.0

• 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
auc_bar	Bar plot of AUCs from validating data sets
auc_stat	Extract AUC statistics in coclustering optimization
auc_violin	Plot extracted AUCs by parameter settings
cluster_cell	Cluster single cells or combination of single cells and bulk
cocluster	Coclustering bulk and single cell data in a single run
coclus_opt	Optimizing coclustering process with two levels of parallelizations available.
coclus_roc	Co-cluster bulk and single cell data Calculate ROC/AUC for the combined bulk and single cell data
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
desired_bulk_shiny	Integrated Shiny App
edit_tar	Edit Targets Files
filter_cell	Filter single cell data separately in a list
filter_data	Filter the Data Matrix
filter_iter	Iteratively filter bulk and single data according to parameters in a data frame.
lis.deg.up.down	A nested list of differentialy-expressed genes (DEGs) detected by different methods
matrix_hm	Matrix Heatmap
mean_auc_bar	Plot mean of extracted AUCs by parameter settings
network	Visualize a Target Assayed Item in a Network Graph
norm_data	Normalize Sequencing Count Matrix
norm_multi	Normalize one or multiple count data sets.
plot_dim	Plotting single cells in reduced dimensionalities
profile_gene	Plot Gene Expression Profiles in a Data Frame
random_para	Generate random combinations of parameter settings
read_cache	Read R Objects from Cache
read_fr	Import Data from Tabular Files
read_hdf5	Read Data from the Shiny App Database
reduce_rep	Reduce sample replicates
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
spd_auc_violin	Violin plot of extracted AUCs by top spd.sets
submatrix	Subset Target Assayed Items and Their Nearest Neighbors
sub_asg	Subset the bulk-cell assignments
sub_data	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