# A Spatial Model of Intra-Tumor Heterogeneity

## Documentation for package ‘SITH’ version 1.1.0

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

## Help Pages

SITH-package | Visualize and analyze intratumor heterogeneity using a spatial model of tumor growth
bulkSample | Simulate bulk sampling
plotSlice | 2D cross section of the simulated tumor
progressionChain | Create a linear chain graph to describe the order of mutations
progressionDAG_from_igraph | Define the progression of mutations from an 'igraph' object
randomBulkSamples | Simulate multi-region bulk sampling
randomNeedles | Simulate fine needle aspiration
randomSingleCells | Simulate single cell sequencing data
simulateTumor | Spatial simulation of tumor growth
singleCell | Simulate single cell sequencing data
SITH | Visualize and analyze intratumor heterogeneity using a spatial model of tumor growth
spatialDistribution | Quantify the spatial distribution of mutants
visualizeTumor | Interactive visualization of the simulated tumor