Package: escheR 1.13.0

Boyi Guo

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.

Authors:Boyi Guo [aut, cre], Stephanie C. Hicks [aut], Erik D. Nelson [ctb]

escheR_1.13.0.tar.gz
escheR_1.13.0.zip(r-4.7)escheR_1.13.0.zip(r-4.6)escheR_1.13.0.zip(r-4.5)
escheR_1.13.0.tgz(r-4.6-any)escheR_1.13.0.tgz(r-4.5-any)
escheR_1.13.0.tar.gz(r-4.7-any)escheR_1.13.0.tar.gz(r-4.6-any)
escheR_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
escheR/json (API)
NEWS

# Install 'escheR' in R:
install.packages('escheR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/boyiguo1/escher/issues

On BioConductor:escheR-1.13.0(bioc 3.24)escheR-1.12.0(bioc 3.23)

spatialsinglecelltranscriptomicsvisualizationsoftwaremultidimensionalsingle-cellspatial-omics

7.14 score 8 stars 1 packages 290 scripts 440 downloads 6 exports 67 dependencies

Last updated from:67f778c50b. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE256
linux-devel-x86_64OK421
source / vignettesOK436
linux-release-x86_64OK421
macos-release-arm64OK206
macos-oldrel-arm64OK214
windows-develOK406
windows-releaseOK374
windows-oldrelOK412
wasm-releaseOK214

Exports:add_filladd_fill_binadd_groundadd_ground_binadd_symbolmake_escheR

Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydplyrfarverfastmapfilelockgenericsGenomicRangesggplot2gluegtablehttr2IRangesisobandlabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6rappdirsRColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVector

Beyond Sequence-based Spatially-Resolved Data

Rendered frommore_than_visium.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-11-14
Started: 2023-09-20

Getting Started with escheR

Rendered fromSRT_eg.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-01-12
Started: 2023-03-24

Readme and manuals

Help Manual

Help pageTopics
Check if rowData(spe) contains reserved name.contain_reserved_col_name
Adding fill to highlight the figure in the spatial mapadd_fill add_fill_bin
Adding border to highlight the ground in the spatial mapadd_ground add_ground_bin
Adding symbols to each spot in the spatial mapadd_symbol
Create a new spatial map for spatial transcriptomics datamake_escheR make_escheR.data.frame make_escheR.SingleCellExperiment make_escheR.SpatialExperiment