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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schex_1.27.0.tgz(r-4.6-any)schex_1.27.0.tgz(r-4.5-any)
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schex_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
schex/json (API)
NEWS

# 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)

software sequencing singlecell dimensionreduction visualization immunooncology dataimport

9.12 score 76 stars 2 packages 146 scripts 464 downloads 10 exports 66 dependencies

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

Target	Result	Time
bioc-checks	NOTE	258
linux-devel-x86_64	WARNING	524
source / vignettes	OK	334
linux-release-x86_64	WARNING	515
macos-release-arm64	WARNING	302
macos-oldrel-arm64	WARNING	317
windows-devel	WARNING	1642
windows-release	WARNING	1245
windows-oldrel	WARNING	1688
wasm-release	OK	231

Exports:make_hexbin make_hexbin_label plot_hexbin_bivariate plot_hexbin_density plot_hexbin_fc plot_hexbin_feature plot_hexbin_feature_plus plot_hexbin_interact plot_hexbin_meta plot_hexbin_meta_plus

Dependencies:abind base64enc Biobase BiocGenerics class classInt cli cluster concaveman cpp11 curl DBI DelayedArray dplyr e1071 entropy farver generics GenomicRanges ggforce ggplot2 glue gtable hexbin IRanges isoband jsonlite KernSmooth labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats pillar pkgconfig polyclip proxy R6 RColorBrewer Rcpp rlang s2 S4Arrays S4Vectors S7 scales Seqinfo sf SingleCellExperiment SparseArray SummarizedExperiment systemfonts tibble tidyselect tweenr units utf8 V8 vctrs viridisLite withr wk XVector

Using schex with Seurat

Rendered fromSeurat_to_SCE.Rmdusingknitr::rmarkdownon May 30 2026.

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

Plotting single cell data with schex

Saskia Freytag

Rendered fromusing_schex.Rmdusingknitr::rmarkdownon May 30 2026.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bivariate binning of single cell data into hexagon cells.	make_hexbin make_hexbin,SingleCellExperiment-method
Group label plot position.	make_hexbin_label
Plot of feature expression and uncertainty of single cells in bivariate hexagon cells.	plot_hexbin_bivariate
Plot of density of observations from single cell data in bivariate hexagon cells.	plot_hexbin_density
Plot of fold change of selected gene in single cell data using bivariate hexagon cells.	plot_hexbin_fc
Plot of feature expression of single cells in bivariate hexagon cells.	plot_hexbin_feature
Plot of gene expression and meta data of single cell data in bivariate hexagon cells.	plot_hexbin_feature_plus
Plot of interaction of expression of single cells in bivariate hexagon cells.	plot_hexbin_interact
Plot of meta data of single cell data in bivariate hexagon cells.	plot_hexbin_meta
Plot of meta data with annotation of single cell data in bivariate hexagon cells.	plot_hexbin_meta_plus
schex: A package for plotting hexbin plots for single cell omics data.	schex