scCustomize-package: scCustomize: Custom Visualizations & Functions for...
In scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
scCustomize-package R Documentation
scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
Description
Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.5706430")} RRID:SCR_024675.
Package options
scCustomize uses the following options() to configure behavior:
scCustomize_warn_raster_iterativeShow message about setting raster parameter
in Iterate_FeaturePlot_scCustom if raster = FALSE and single_pdf = TRUE
due to large file sizes.
scCustomize_warn_raster_LIGERShow warning about rasterization of points in
DimPlot_LIGER due to new functionality compared to LIGER.
scCustomize_warn_na_cutoffShow message about properly setting na_cutoff parameter in FeaturePlot_scCustom.
#'
scCustomize_warn_zero_na_cutoffShow message about properly setting na_cutoff parameter in FeaturePlot_scCustom if na_cutoff is set to exactly zero.
scCustomize_warn_vln_raster_iterativeShow message about Iterate_VlnPlot_scCustom
when pt.size > 0 due to current lack of raster support in VlnPlot
scCustomize_warn_LIGER_dim_labelsShow message about DimPlot_LIGER
parameter reduction_label as LIGER objects do not store dimensionality reduction name and
and therefore needs to be set manually.
scCustomize_warn_DimPlot_split_typeShow message about DimPlot_scCustom
parameter split.by and split_seurat to alert user to difference in returned plots between
scCustomize and Seurat.
scCustomize_warn_FeatureScatter_split_typeShow message about FeatureScatter_scCustom
parameter split.by and split_seurat to alert user to difference in returned plots between
scCustomize and Seurat.
scCustomize_warn_LIGER_dim_labels_plotFactorsShow message about plotFactors_scCustom
parameter reduction_label as LIGER objects do not store dimensionality reduction name and
and therefore needs to be set manually.
Author(s)
Maintainer: Samuel Marsh sccustomize@gmail.com (ORCID)
Other contributors:
Ming Tang tangming2005@gmail.com [contributor]
Velina Kozareva [contributor]
Lucas Graybuck lucasg@alleninstitute.org [contributor]
Zoe Clarke zoe.clarke@utoronto.ca (ORCID) [contributor]
See Also
Useful links:
-
-
- \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.5706431")}
Report bugs at https://github.com/samuel-marsh/scCustomize/issues
scCustomize documentation built on Aug. 26, 2025, 9:08 a.m.
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| scCustomize-package | R Documentation |
scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
Description
Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.5706430")} RRID:SCR_024675.
Package options
scCustomize uses the following options() to configure behavior:
scCustomize_warn_raster_iterativeShow message about setting
rasterparameter inIterate_FeaturePlot_scCustomifraster = FALSEandsingle_pdf = TRUEdue to large file sizes.scCustomize_warn_raster_LIGERShow warning about rasterization of points in
DimPlot_LIGERdue to new functionality compared to LIGER.scCustomize_warn_na_cutoffShow message about properly setting
na_cutoffparameter inFeaturePlot_scCustom.
#'
scCustomize_warn_zero_na_cutoffShow message about properly setting
na_cutoffparameter inFeaturePlot_scCustomifna_cutoffis set to exactly zero.scCustomize_warn_vln_raster_iterativeShow message about
Iterate_VlnPlot_scCustomwhenpt.size > 0due to current lack of raster support inVlnPlotscCustomize_warn_LIGER_dim_labelsShow message about
DimPlot_LIGERparameterreduction_labelas LIGER objects do not store dimensionality reduction name and and therefore needs to be set manually.scCustomize_warn_DimPlot_split_typeShow message about
DimPlot_scCustomparametersplit.byandsplit_seuratto alert user to difference in returned plots between scCustomize and Seurat.scCustomize_warn_FeatureScatter_split_typeShow message about
FeatureScatter_scCustomparametersplit.byandsplit_seuratto alert user to difference in returned plots between scCustomize and Seurat.scCustomize_warn_LIGER_dim_labels_plotFactorsShow message about
plotFactors_scCustomparameterreduction_labelas LIGER objects do not store dimensionality reduction name and and therefore needs to be set manually.
Author(s)
Maintainer: Samuel Marsh sccustomize@gmail.com (ORCID)
Other contributors:
Ming Tang tangming2005@gmail.com [contributor]
Velina Kozareva [contributor]
Lucas Graybuck lucasg@alleninstitute.org [contributor]
Zoe Clarke zoe.clarke@utoronto.ca (ORCID) [contributor]
See Also
Useful links:
- \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.5706431")}
Report bugs at https://github.com/samuel-marsh/scCustomize/issues
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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