mapscape
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see mapscape.
mapscape
Bioconductor version: 3.17
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("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 |
Details
biocViews | Software, Visualization |
Version | 1.24.0 |
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) |
System Requirements | |
URL |
See More
Suggests | knitr, rmarkdown |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | mapscape_1.24.0.tar.gz |
Windows Binary | mapscape_1.24.0.zip |
macOS Binary (x86_64) | mapscape_1.24.0.tgz |
macOS Binary (arm64) | mapscape_1.24.0.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 |
Old Source Packages for BioC 3.17 | Source Archive |