# Topic Inference to Identify Tissue Architecture in Multiplexed Images

## Documentation for package ‘SpaTopic’ version 1.3.1

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

## Help Pages

SpaTopic-package | SpaTopic: Spatial Topic Modeling for Multiplexed Images
frex_topic | Calculate FREX ranked words and values for a topic
label_topics | Label topics function
lift_topic | Calculate lift ranked words and values for a topic
lung5 | Example input data for 'SpaTopic'
print.SpaTopic | Print method for SpaTopic objects
prob_topic | Calculate highest probability words and values for a topic
score_topic | Calculate score ranked words and values for a topic
Seurat5obj_to_SpaTopic | Convert a Seurat v5 object as the input of 'SpaTopic'
SpaTopic | SpaTopic: Spatial Topic Modeling for Multiplexed Images
SpaTopic-class | A class of the output from 'SpaTopic'
SpaTopic-Package | SpaTopic: Spatial Topic Modeling for Multiplexed Images
SpaTopic_inference | 'SpaTopic': fast topic inference to identify tissue architecture in multiplexed images
spatopic_message | Format messages for SpaTopic package
stratified_sampling_3D_via_2D | Spatially stratified random sample points from a 3D image using 2D slicing.
stratified_sampling_sf | Spatially stratified random sample points from an image.