Embedding and Clustering with Alignment for Spatial Datasets

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Documentation for package ‘PRECAST’ version 1.6.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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.
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
volinPlot	Volin/boxplot plot