# Embedding and Clustering with Alignment for Spatial Omics Datasets

## Documentation for package ‘PRECAST’ version 1.8

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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.
getneighborhood_fast | getneighborhood_fast
Human_HK_genes | Human housekeeping genes database
ICM.EM | ICM-EM algorithm implementation
ICM.EM_structure | ICM-EM algorithm implementation with organized paramters
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
PRECAST | Fit a PRECAST model
PRECASTObj | A simple PRECASTObj for example
PRECASTObj-class | Each PRECASTObj object has a number of slots which store information.
selectIntFeatures | Select common genes for multiple data batches
SelectModel | Select best PRECAST model from candidated models
SelectModel.PRECASTObj | Select best PRECAST model from candidated models
SelectModel.SeqK_PRECAST_Object | Select best PRECAST model from candidated models
SpaPlot | Spatial heatmap
sp_means_Rcpp | Calculate column-wise or row-wise mean
sp_sums_Rcpp | Calculate column-wise or row-wise sum
volinPlot | Volin/boxplot plot