MapScape vignette

MapScape is a visualization tool for spatial clonal evolution. MapScape displays a cropped anatomical image surrounded by two representations of each tumour sample representing the distribution of clones throughout anatomic space. The first, a cellular aggregate or donut view, displays the prevalence of each clone. The second shows a skeleton of the patient’s clonal phylogeny while highlighting only those clones present in the sample.

Note: the cellular aggregate does not accurately represent the positions of clones within a sample. We therefore provide the alternative donut chart view as a less artistic representation of the tumour sample. See the Interactivity section below for instructions to switch between views.

Installation

To install MapScape, type the following commands in R:

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

Examples

Run the examples by:

example("mapscape")

Three visualizations will appear in your browser (optimized for Chrome).

For instance, the first visualization is of metastatic prostate cancer data published in Gundem et al. (2015):