Function reference • SRTpipeline

All functions
`simu_seuList()`	SpatialExperiment object to Seurat object
`AddTSNE()`	Add tSNE embeddings for a SRTProject object
`chooseColors()`	Choose color schema from a palette
`AddUMAP()`	Add UMAP embeddings for a SRTProject object
`transferGeneNames()`	Transfer gene names from one fortmat to the other format
`filter_gene()`	Filter genes for a Seurat object
`filter_spot()`	Filter spots for a Seurat object
`get_top_pathway()`	Get top pathways from enrichment analysis results
`barPlot_enrich()`	Barplot for the enrichment terms
`RCTD_structure()`	Prepare the reference panel data for the RCTD deconvolution analysis
`RCTD_run()`	Perform spatial deconvolution analysis using RCTD model
`model_set_SCMEB()`	Set parameters for SC-MEB model
`model_set_DRSC()`	Set parameters for DR-SC model
`model_set_PRECAST()`	Set parameters for PRECAST model
`getIntegratedData()`	Get the batch-corrected integrated gene expresssions
`SRTProject-class`	SRTProject Class to store SRT datasets
`addProjectSummary()`	Add the summary data for a SRTProject object
`setSRTverbose()`	Determine whether output the information for all functions in SRTpipeline package.
`getSRTVerbose()`	Get the output status
`setSRToutputPrefix()`	Set the Prefix when output informtion
`getSRToutputPrefix()`	Get the Prefix of output information
`CreateSRTProject()`	Create a SRTProject object
`normalizeSRT()`	Normalize the expression count data
`selectVariableFeatures()`	Select variable genes
`AddAdj()`	Add adjacency matrix list for a SRTProject object
`CCHeatMap()`	Plot cluster-by-cluster correlation hetamap
`EmbedPlot()`	Two-dimensional embeddings plot
`model_set_iSCMEB()`	Set parameters for iSC.MEB model
`FindDEGs()`	Find differential expression genes Find differential expression genes by comparing two clusters.
`FindAllDEGs()`	Find differential expression genes for all clusters by comparing one cluster to the remaining clusters.
`AddTrajectory()`	Implement trajectory inference
`AddPCA()`	Add PCA embeddings for a SRTProject object
`cluster_metric()`	Compute adjusted Rand index and normalized mutual information
`Integrate_PRECAST()`	Joint embedding, clustering and alignment for SRT data by fitting a PRECAST model
`Cluster_DRSC()`	Joint embedding and clustering for SRT data by fitting an iSC.MEB model a DR-SC model
`Cluster_SCMEB()`	Spatial clustering for SRT data by fitting a SC-MEB model
`Cluster_Louvain()`	Louvain clustering for a SRT data
`Annotation_SpatialAnno()`	Make annotations for SRT data by fitting a SpatialAnno model
`TrajectEmbedPlot()`	Visualize the inferred pseudotime on embeddings.
`write_fig()`	Save a ggplot object to a PNG figure
`Integrate_iSCMEB()`	Joint clustering and alignment for SRT data by fitting an iSC.MEB model
`vec2list()`	Transfer a vector to a list
`mat2list()`	Transfer a matrix to a list
`matlist2mat()`	Transfer matrix list to a matrix
`getGeneSpotData()`	Get the expression matrix from a SRTProject object
`EachClusterSpaHeatMap()`	Plot spatial cluster heatmap for each data batch
`EachRGBSpaHeatMap()`	Plot spatial RGB heatmaps for a group of SRT data batches
`EachExprSpaHeatMap()`	Plot spatial feature heatmaps for a group of SRT data batches
`EachGCHeatMap()`	Plot gene-by-cell heatmaps for a group of SRT data batches
`model_set_Louvain()`	Set parameters for Louvain model
`model_set_SpatialAnno()`	Set parameters for SpatialAnno model
`topVGs()`	Get the top variables genes
`AddClusters2MetaData()`	Add inferred clusters to the `cellMetaData`
`GCHeatMap()`	Plot gene-by-cell heatmap
`EachEmbedPlot()`	Plot the embeddings for each SRT data
`drawFigs()`	Draw a figure using a group of ggplot objects
`spe2seurat()`	SpatialExperiment object to Seurat object
`spe2seuratList()`	SpatialExperiment object to Seurat list object
`seu2seuList()`	Seurat object to seuratList object
`sce2seurat()`	SingleCellExperiment object to Seurat object

Reference

All functions