mapscape
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see mapscape.
mapscape
Bioconductor version: 3.9
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 "3.6") 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 | 1.8.0 |
| 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_1.8.0.tar.gz |
| Windows Binary | mapscape_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | mapscape_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mapscape |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |