To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

mapscape

DOI: 10.18129/B9.bioc.mapscape    

mapscape

Bioconductor version: Release (3.5)

MapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each sample. The output of MapScape consists of a cropped anatomical image surrounded by two representations of each tumour sample. The first, a cellular aggregate, visually displays the prevalence of each clone. The second shows a skeleton of the clonal phylogeny while highlighting only those clones present in the sample. Together, these representations enable the analyst to visualize the distribution of clones throughout anatomic space.

Author: Maia Smith [aut, cre]

Maintainer: Maia Smith <maiaannesmith at gmail.com>

Citation (from within R, enter citation("mapscape")):

Installation

To install this package, start R and enter:

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

Documentation

HTML R Script MapScape vignette
PDF   Reference Manual

Details

biocViews Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL-3
Depends R (>= 3.3)
Imports htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0)
LinkingTo
Suggests knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source mapscape_1.0.0.tar.gz
Windows Binary mapscape_1.0.0.zip
Mac OS X 10.11 (El Capitan) mapscape_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/mapscape
Package Short Url http://bioconductor.org/packages/mapscape/
Package Downloads Report Download Stats

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