Man pages for jianhaizhang/spatialHeatmap
spatialHeatmap

adj_modComputing adjacency matrix and identifying network modules
aggr_repAggregate "Sample__Condition" Replicates in Data Matrix
aSVG.remote.repoA list of URLs of remote aSVG repos
cell_groupAdd manual cell group labels to SingleCellExperiment
cluster_cellCluster single cells or combination of single cells and bulk
coclus_optOptimization of co-clustering bulk and single cell data
coclusterCo-clustering bulk and single cell data
com_factorCombine Factors in Targets File
covisCo-visualizing spatial heatmaps with single-cell embedding...
custom_shinyCreate Customized spatialHeatmap Shiny Apps
cut_dendroCutting dendrograms
cvt_idConverting gene ids using annotation databases
databaseCreat databases for the Shiny App
data_refCalculating relative expression values
edit_tarEdit Targets Files
filter_dataFiltering the Data Matrix
matrix_hmHierarchical clustering combined with matrix heatmap
networkNetwork graphs
norm_cellNormalizing single cell data
norm_dataNormalize Sequencing Count Matrix
norm_srscJointl normalization of spatially resolved single cell data...
opt_barBar plots of co-clustering optimization results.
optimal_kUsing the elbow method to find the optimal number of clusters...
opt_settingBar plots of co-clustering optimization results.
opt_violinViolin plots of co-clustering validation results
plot_dimEmbedding plots of single cells/bulk tissues after...
plot_kmeansPlotting the clusters returned by K-means clustering
plot_metaMeta function for plotting spatial heatmaps or co-visualizing...
process_cell_metaProcessing single cell RNA-seq count data
qc_cellQuality control in single cell data
read_cacheRead R Objects from Cache
read_frImport Data from Tabular Files
read_svgParsing annotated SVG (aSVG) files
reduce_dimReducing dimensionality in count data
reduce_repReduce sample replicates
return_featureReturn aSVG Files Relevant to Target Features
save_cacheSave R Objects in Cache
shiny_shmIntegrated Shiny App
shmPlot Spatial Heatmaps
SpatialEnrichmentIdentifying spatially enriched or depleted biomolecules
spatialHeatmap-packagespatialHeatmap Spatial Heatmap, Spatial Enrichment, Data...
spatial_hmPlot Spatial Heatmaps
SPHMThe SPHM class
SPHMMethodsMethods for S4 class 'SPHM'
submatrixSubsetting data matrix
SVGThe SVG class for storing annotated SVG (aSVG) instances
SVGMethodsMethods for S4 class 'SVG'
true_bulkAssign true bulk to cells in 'colData' slot.
update_featureUpdate aSVG Spatial Features
write_svgExporting each spatial heatmap to a separate SVG file
jianhaizhang/spatialHeatmap documentation built on July 31, 2024, 2:59 a.m.