spatialHeatmap


[Up] [Top]

Documentation for package ‘spatialHeatmap’ version 2.2.0

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