Package: escheR 1.7.0
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_1.7.0.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')) |
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
Last updated 23 days agofrom:6c6c207ce3. Checks:OK: 1 WARNING: 6. Indexed: yes.
Target | Result | Date |
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Doc / Vignettes | OK | Nov 18 2024 |
R-4.5-win | WARNING | Nov 18 2024 |
R-4.5-linux | WARNING | Nov 18 2024 |
R-4.4-win | WARNING | Nov 18 2024 |
R-4.4-mac | WARNING | Nov 18 2024 |
R-4.3-win | WARNING | Nov 18 2024 |
R-4.3-mac | WARNING | Nov 18 2024 |
Exports:add_filladd_fill_binadd_groundadd_ground_binadd_symbolmake_escheR
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpurrrR6RColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsscalesSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
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 |