escheR
This is the development version of escheR; for the stable release version, see escheR.
Unified multi-dimensional visualizations with Gestalt principles
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Boyi Guo <boyi.guo.work at gmail.com>
citation("escheR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.7.0 |
| 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_1.7.0.tar.gz |
| Windows Binary (x86_64) | escheR_1.7.0.zip |
| macOS Binary (x86_64) | escheR_1.7.0.tgz |
| macOS Binary (arm64) | escheR_1.7.0.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 |