escheR

DOI: 10.18129/B9.bioc.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 (3.19)

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>

Installation

To install this package, start R (version "4.4") 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")

 

HTML	R Script	beyond_visium
HTML	R Script	Getting Start with `escheR`
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	SingleCell, Software, Spatial, Transcriptomics, Visualization
Version	1.3.1
In Bioconductor since	BioC 3.17 (R-4.3) (0.5 years)
License	MIT + file LICENSE
Depends	ggplot2, R (>= 4.3)
Imports	SpatialExperiment(>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment
LinkingTo
Suggests	STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin
SystemRequirements
Enhances
URL	https://github.com/boyiguo1/escheR
BugReports	https://github.com/boyiguo1/escheR/issues
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	escheR_1.3.1.tar.gz
Windows Binary	escheR_1.3.1.zip
macOS Binary (x86_64)	escheR_1.3.1.tgz
macOS Binary (arm64)
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