R package version 1.2.0
The following is required for installing the package:
R
version 4.0.0 or newer.- Package
Rcpp
which can be downloaded from CRAN by runninginstall.packages("Rcpp")
from the console. - Package
rgl
is strongly recommended for visualizations can be downloaded from CRAN by runninginstall.packages(rgl)
from the console.- macOS users may have to install Xquartz
before installing
rgl
.
- macOS users may have to install Xquartz
before installing
See the package documentation for a complete list of dependencies.
As the package is on CRAN, it can be installed by running
install.packages(SITH)
from the command line.
Alternatively, 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.
- Contains a 3D simulator of spatial tumor growth and mutation, similar
to the model described in this
paper.
- The simulator is written in C++ since it is computationally expensive.
- A tumor with 1 million cells can be simulated in under a minute on a standard desktop computer.
- Simulation of the tumor under targeted therapy.
- 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.
set.seed(1126490984)
library(SITH)
library(rgl)
Generate a tumor with
out <- simulateTumor(max_pop = 1000000, verbose = FALSE)
visualizeTumor(out, background = "white")
rgl::view3d(zoom = 0.66)
visualizeTumor(out, background = "white", plot.type = "heat")
rgl::view3d(zoom = 0.66)
If you use SITH
in your work, please cite:
Nicol, P.B., Barabasi, D.L., Coombes, K.R. and Asiaee, A. (2022). SITH: an R package for visualizing and analyzing a spatial model of intratumor heterogeneity. Computational and Systems Oncology. Vol 2(2), pg. e1033. https://doi.org/10.1002/cso2.1033.