README.md

TimeScape is a visualization tool for temporal clonal evolution.

Development Instructions

To debug / develop timescape, run the following:

# load the up-to-date local code
source("./R/timescape.R")

# run your timescape commands, example below:
tree_edges <- read.csv(system.file("extdata", "AML_tree_edges.csv", package = "timescape"))
clonal_prev <- read.csv(system.file("extdata", "AML_clonal_prev.csv", package = "timescape"))
mutations <- read.csv(system.file("extdata", "AML_mutations.csv", package = "timescape"))
perturbations <- data.frame(pert_name = c("Chemotherapy"), prev_tp = c("Diagnosis"), frac = c(0.1))
timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, perturbations = perturbations, height=260)

Installation

To install TimeScape, type the following commands in R:

# try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("timescape")

Examples

Run the examples by:

example("timescape")

Documentation

To view the documentation for TimeScape, type the following command in R:

?timescape

or:

browseVignettes("timescape") 

References

TimeScape was developed at the Shah Lab for Computational Cancer Biology at the BC Cancer Research Centre.