escheR
Unified multi-dimensional visualizations with Gestalt principles
Bioconductor version: Release (3.19)
The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.
Author: Boyi Guo [aut, cre] , Stephanie C. Hicks [aut] , Erik D. Nelson [ctb]
Maintainer: Boyi Guo <boyi.guo.work at gmail.com>
citation("escheR")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("escheR")
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("escheR")
beyond_visium | HTML | R Script |
Getting Start with `escheR` | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | SingleCell, Software, Spatial, Transcriptomics, Visualization |
Version | 1.4.0 |
In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
License | MIT + file LICENSE |
Depends | ggplot2, R (>= 4.3) |
Imports | SpatialExperiment(>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment |
System Requirements | |
URL | https://github.com/boyiguo1/escheR |
Bug Reports | https://github.com/boyiguo1/escheR/issues |
See More
Suggests | STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | SpotSweeper |
Suggests Me | tpSVG |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | escheR_1.4.0.tar.gz |
Windows Binary | escheR_1.4.0.zip (64-bit only) |
macOS Binary (x86_64) | escheR_1.4.0.tgz |
macOS Binary (arm64) | escheR_1.4.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/escheR |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/escheR |
Bioc Package Browser | https://code.bioconductor.org/browse/escheR/ |
Package Short Url | https://bioconductor.org/packages/escheR/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.19 | Source Archive |