PRECAST1.7 package

Add embeddings for a Seurat object

Add adjacency matrix list for a PRECASTObj object

Add model settings for a PRECASTObj object

Add tSNE embeddings for a Seurat object

Add UMAP embeddings for a Seurat object

Boxplot for a matrix

Choose color schema from a palette

Coordinates rotation for visualization

Create the PRECAST object with preprocessing step.

Low-dimensional embeddings' plot

Heatmap for spots-by-feature matrix

Draw a figure using a group of ggplot objects

Spatial expression heatmap

Set the first letter of a string vector to captial

Calculate adjacency matrix by user-specified number of neighbors

Calculate adjacency matrix for regular spatial coordinates.

ICM-EM algorithm implementation with organized paramters

ICM-EM algorithm implementation

Integrate multiple SRT data

PRECAST model setting

Spatial RGB heatmap

Scatter plot for two-dimensional embeddings

A simple PRECASTObj for example

Fit a PRECAST model

Select common genes for multiple data batches

Select best PRECAST model from candidated models

Spatial heatmap

Volin/boxplot plot