A Spatial Model of Intra-Tumor Heterogeneity (SITH)

R package version 1.0.1.1 (1.0.1 on CRAN).

Installation

The following is required for installing the package:

• R version 3.6.0 or newer.
• Package Rcpp which can be downloaded from CRAN by running install.packages("Rcpp") from the console.
• Package rgl is strongly recommended for visualizations can be downloaded from CRAN by running install.packages(rgl) from the console.
  • macOS users may have to install Xquartz before installing rgl.

See the package documentation for a complete list of dependencies.

The official release is on CRAN, and can be installed by running install.packages(SITH) from the command line.

The newest version of the package can be installed directly from this repository by first installing devtools (run install.packages(devtools)) and then running install_github("phillipnicol/SITH") from the console.

Reference manual and vignette

Refer to the official CRAN page to view the package vignette and reference manual.

Features

• Contains a 3D simulator of spatial tumor growth and mutation, similar to the model described in this paper.
  • The main simulations are in C++ for performance.
  • A tumor with 1 million cells can be simulated in under a minute on a standard desktop computer.
• 3D interactive visualizations of the simulated tumor using rgl.
  • Option to color regions with high mutation red and regions with low mutation blue.
  • 2D cross section
• Summary of the spatial distribution of mutations throughout the tumor.
  • Creates graphs that show how genetic diversity changes in different spatial regions.
• Create synthetic bulk and single-cell sequencing data from the simulated tumor.
  • Users can specify what part of the tumor the samples are taken from.

Features (Github version only)

• Simulations with user-defined mutation types (instead of assuming infinite alleles hypothesis). See simulateTumorMTBP(), vignette soon to come.
• More realistic bulk sequencing procedure, allowing user to set coverage.

Future features

• Metastatic seeding.
• Simulation of therapeutic and surgical procedures.

Demo

set.seed(1126490984)
library(SITH)
library(rgl)

Generate a tumor with 1000000 cells:

out <- simulateTumor(N = 1000000, verbose = FALSE)

Visualize the tumor with each unique genotype colored differently:

visualizeTumor(out, background = "white")
rgl::view3d(zoom = 0.66)

Color regions of low mutation blue and regions of high mutation red:

visualizeTumor(out, background = "white", plot.type = "heat")
rgl::view3d(zoom = 0.66)