Package: escheR 1.7.0

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_1.7.0.tar.gz
escheR_1.7.0.zip(r-4.5)escheR_1.7.0.zip(r-4.4)escheR_1.7.0.zip(r-4.3)
escheR_1.7.0.tgz(r-4.4-any)escheR_1.7.0.tgz(r-4.3-any)
escheR_1.7.0.tar.gz(r-4.5-noble)escheR_1.7.0.tar.gz(r-4.4-noble)
escheR_1.7.0.tgz(r-4.4-emscripten)escheR_1.7.0.tgz(r-4.3-emscripten)
escheR.pdf |escheR.html
escheR/json (API)
NEWS

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

Peer review:

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

On BioConductor:escheR-1.7.0(bioc 3.21)escheR-1.6.0(bioc 3.20)

spatialsinglecelltranscriptomicsvisualizationsoftwaremultidimensionalsingle-cellspatial-omics

6.89 score 6 stars 1 packages 109 scripts 198 downloads 6 exports 78 dependencies

Last updated 23 days agofrom:6c6c207ce3. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:add_filladd_fill_binadd_groundadd_ground_binadd_symbolmake_escheR

Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpurrrR6RColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsscalesSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Beyond Sequence-based Spatially-Resolved Data

Rendered frommore_than_visium.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Getting Started with escheR

Rendered fromSRT_eg.Rmdusingknitr::rmarkdownon Nov 18 2024.

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