Function reference • PRECAST

All functions
`AddAdjList()`	Add adjacency matrix list for a PRECASTObj object
`AddParSetting()`	Add model settings for a PRECASTObj object
`AddTSNE()`	Add tSNE embeddings for a Seurat object
`AddUMAP()`	Add UMAP embeddings for a Seurat object
`Add_embed()`	Add embeddings for a Seurat object
`boxPlot()`	Boxplot for a matrix
`chooseColors()`	Choose color schema from a palette
`coordinate_rotate()`	Coordinates rotation for visualization
`CreatePRECASTObject()`	Create the PRECAST object with preprocessing step.
`dimPlot()`	Low-dimensional embeddings' plot
`doHeatmap()`	Heatmap for spots-by-feature matrix
`drawFigs()`	Draw a figure using a group of ggplot objects
`featurePlot()`	Spatial expression heatmap
`firstup()`	Set the first letter of a string vector to captial
`getAdj_fixedNumber()`	Calculate adjacency matrix by user-specified number of neighbors
`getAdj_reg()`	Calculate adjacency matrix for regular spatial coordinates.
`Human_HK_genes`	Human housekeeping genes database
`ICM.EM_structure()`	ICM-EM algorithm implementation with organized paramters
`ICM.EM()`	ICM-EM algorithm implementation
`IntegrateSpaData()`	Integrate multiple SRT data
`model_set()`	PRECAST model setting
`Mouse_HK_genes`	Mouse housekeeping genes database
`plot_RGB()`	Spatial RGB heatmap
`plot_scatter()`	Scatter plot for two-dimensional embeddings
`PRECASTObj`	A simple PRECASTObj for example
`PRECAST()`	Fit a PRECAST model
`PRECASTObj-class`	Each PRECASTObj object has a number of slots which store information.
`selectIntFeatures()`	Select common genes for multiple data batches
`SelectModel(<SeqK_PRECAST_Object>)` `SelectModel(<PRECASTObj>)`	Select best PRECAST model from candidated models
`SpaPlot()`	Spatial heatmap
`volinPlot()`	Volin/boxplot plot

Reference

All functions