mapscape

DOI: 10.18129/B9.bioc.mapscape    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see mapscape.

mapscape

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mapscape")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mapscape")

 

HTML	R Script	MapScape vignette
PDF		Reference Manual

Details

biocViews	Software, Visualization
Version	1.20.0
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 years)
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
Links To Me
Build Report

Package Archives

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

Source Package	mapscape_1.20.0.tar.gz
Windows Binary	mapscape_1.20.0.zip
macOS Binary (x86_64)	mapscape_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mapscape
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mapscape
Package Short Url	https://bioconductor.org/packages/mapscape/
Package Downloads Report	Download Stats