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 |