Package: schex 1.21.0

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]

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schex.pdf |schex.html✨
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-1.21.0(bioc 3.21)schex-1.20.0(bioc 3.20)

software sequencing singlecell dimensionreduction visualization immunooncology dataimport

9.10 score 73 stars 2 packages 95 scripts 380 downloads 10 exports 79 dependencies

Last updated 2 months agofrom:6af9fd53d1. Checks:OK: 3 NOTE: 2 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 14 2024
R-4.5-win	NOTE	Dec 14 2024
R-4.5-linux	NOTE	Dec 14 2024
R-4.4-win	OK	Dec 14 2024
R-4.4-mac	ERROR	Dec 14 2024
R-4.3-win	OK	Dec 14 2024
R-4.3-mac	ERROR	Dec 14 2024

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 askpass Biobase BiocGenerics class classInt cli cluster colorspace concaveman cpp11 crayon curl DBI DelayedArray dplyr e1071 entropy fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggforce ggplot2 glue gtable hexbin httr IRanges isoband jsonlite KernSmooth labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig polyclip proxy R6 RColorBrewer Rcpp RcppEigen rlang s2 S4Arrays S4Vectors scales sf SingleCellExperiment SparseArray SummarizedExperiment sys systemfonts tibble tidyselect tweenr UCSC.utils units utf8 V8 vctrs viridisLite withr wk XVector zlibbioc

Using schex with Seurat

Rendered fromSeurat_to_SCE.Rmdusingknitr::rmarkdownon Dec 14 2024.

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

Plotting single cell data with schex

Saskia Freytag

Rendered fromusing_schex.Rmdusingknitr::rmarkdownon Dec 14 2024.

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