recipe bioconductor-escher

Unified multi-dimensional visualizations with Gestalt principles






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.

package bioconductor-escher

(downloads) docker_bioconductor-escher



depends bioconductor-singlecellexperiment:


depends bioconductor-spatialexperiment:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-ggplot2:

depends r-rlang:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-escher

and update with::

   mamba update bioconductor-escher

To create a new environment, run:

mamba create --name myenvname bioconductor-escher

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-escher/tags`_ for valid values for ``<tag>``)

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