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mapscape

mapscape


Bioconductor version: Release (3.18)

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 (version "4.3") 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")
MapScape vignette HTML R Script
Reference Manual PDF

Details

biocViews Software, Visualization
Version 1.26.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends R (>= 3.3)
Imports htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0)
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Suggests knitr, rmarkdown
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Package Archives

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

Source Package mapscape_1.26.0.tar.gz
Windows Binary mapscape_1.26.0.zip
macOS Binary (x86_64) mapscape_1.26.0.tgz
macOS Binary (arm64) mapscape_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/mapscape
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mapscape
Bioc Package Browser https://code.bioconductor.org/browse/mapscape/
Package Short Url https://bioconductor.org/packages/mapscape/
Package Downloads Report Download Stats