Package: escheR 1.13.0

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:
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
Last updated from:67f778c50b. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 256 | ||
| linux-devel-x86_64 | OK | 421 | ||
| source / vignettes | OK | 436 | ||
| linux-release-x86_64 | OK | 421 | ||
| macos-release-arm64 | OK | 206 | ||
| macos-oldrel-arm64 | OK | 214 | ||
| windows-devel | OK | 406 | ||
| windows-release | OK | 374 | ||
| windows-oldrel | OK | 412 | ||
| wasm-release | OK | 214 |
Exports:add_filladd_fill_binadd_groundadd_ground_binadd_symbolmake_escheR
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydplyrfarverfastmapfilelockgenericsGenomicRangesggplot2gluegtablehttr2IRangesisobandlabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6rappdirsRColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Check if rowData(spe) contains reserved name | .contain_reserved_col_name |
| Adding fill to highlight the figure in the spatial map | add_fill add_fill_bin |
| Adding border to highlight the ground in the spatial map | add_ground add_ground_bin |
| Adding symbols to each spot in the spatial map | add_symbol |
| Create a new spatial map for spatial transcriptomics data | make_escheR make_escheR.data.frame make_escheR.SingleCellExperiment make_escheR.SpatialExperiment |
