Package: schex 1.27.0

Saskia Freytag

schex: Hexbin plots for single cell omics data

Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley.

Authors:Saskia Freytag [aut, cre], Wancheng Tang [ctb], Zimo Peng [ctb], Jingxiu Huang [ctb]

schex_1.27.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
schex/json (API)

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

Bug tracker:https://github.com/saskiafreytag/schex/issues

On BioConductor:schex-1.27.0(bioc 3.24)schex-1.26.0(bioc 3.23)

softwaresequencingsinglecelldimensionreductionvisualizationimmunooncologydataimport

9.14 score 76 stars 2 packages 153 scripts 10 exports 66 dependencies

Last updated from:da21fcbc4d. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE228
linux-devel-x86_64WARNING523
source / vignettesOK387
linux-release-x86_64WARNING534
macos-release-arm64WARNING315
macos-oldrel-arm64WARNING260
windows-develWARNING1230
windows-releaseWARNING1346
windows-oldrelWARNING1367
wasm-releaseOK258

Exports:make_hexbinmake_hexbin_labelplot_hexbin_bivariateplot_hexbin_densityplot_hexbin_fcplot_hexbin_featureplot_hexbin_feature_plusplot_hexbin_interactplot_hexbin_metaplot_hexbin_meta_plus

Dependencies:abindbase64encBiobaseBiocGenericsclassclassIntcliclusterconcavemancpp11curlDBIDelayedArraydplyre1071entropyfarvergenericsGenomicRangesggforceggplot2gluegtablehexbinIRangesisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatspillarpkgconfigpolyclipproxyR6RColorBrewerRcpprlangs2S4ArraysS4VectorsS7scalesSeqinfosfSingleCellExperimentSparseArraySummarizedExperimentsystemfontstibbletidyselecttweenrunitsutf8V8vctrsviridisLitewithrwkXVector

Using schex with Seurat
Load libraries | Setup single cell data | Perform dimensionality reductions | Converting to SingleCellExperiment object | Plotting single cell data | Calculate hexagon cell representation | Plot number of cells/nuclei in each hexagon cell | Plot meta data in hexagon cell representation | Plot gene expression in hexagon cell representation | Understanding schex output as ggplot objects
Rendered fromSeurat_to_SCE.Rmdusingknitr::rmarkdown

Last update: 2024-01-30
Started: 2024-01-30

Plotting single cell data with schex
Load libraries | Setup single cell data | Filtering | Normalization | Dimension reduction | Clustering | Plotting single cell data | Calculate hexagon cell representation | Plot number of cells/nuclei in each hexagon cell | Plot meta data in hexagon cell representation | Plot gene expression in hexagon cell representation | Understanding schex output as ggplot objects
Rendered fromusing_schex.Rmdusingknitr::rmarkdown

Last update: 2024-01-30
Started: 2019-06-25