This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

mapscape

This is the development version of mapscape; for the stable release version, see mapscape.

mapscape

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.25.0
In Bioconductor since BioC 3.5 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.3)
Imports htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0)
Linking To
Suggests knitr, rmarkdown
System Requirements
Enhances
URL
See More
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_1.25.0.tar.gz
Windows Binary mapscape_1.25.0.zip
macOS Binary (x86_64) mapscape_1.25.0.tgz
macOS Binary (arm64) mapscape_1.25.0.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