scCustomize-package {scCustomize} | 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" doi:10.5281/zenodo.5706430 RRID:SCR_024675.
Package options
scCustomize uses the following options()
to configure behavior:
scCustomize_warn_raster_iterative
Show message about setting
raster
parameter inIterate_FeaturePlot_scCustom
ifraster = FALSE
andsingle_pdf = TRUE
due to large file sizes.scCustomize_warn_raster_LIGER
Show warning about rasterization of points in
DimPlot_LIGER
due to new functionality compared to LIGER.scCustomize_warn_na_cutoff
Show message about properly setting
na_cutoff
parameter inFeaturePlot_scCustom
.
#'
scCustomize_warn_zero_na_cutoff
Show message about properly setting
na_cutoff
parameter inFeaturePlot_scCustom
ifna_cutoff
is set to exactly zero.scCustomize_warn_vln_raster_iterative
Show message about
Iterate_VlnPlot_scCustom
whenpt.size > 0
due to current lack of raster support inVlnPlot
scCustomize_warn_LIGER_dim_labels
Show message about
DimPlot_LIGER
parameterreduction_label
as LIGER objects do not store dimensionality reduction name and and therefore needs to be set manually.scCustomize_warn_DimPlot_split_type
Show message about
DimPlot_scCustom
parametersplit.by
andsplit_seurat
to alert user to difference in returned plots between scCustomize and Seurat.scCustomize_warn_FeatureScatter_split_type
Show message about
FeatureScatter_scCustom
parametersplit.by
andsplit_seurat
to alert user to difference in returned plots between scCustomize and Seurat.scCustomize_warn_LIGER_dim_labels_plotFactors
Show message about
plotFactors_scCustom
parameterreduction_label
as LIGER objects do not store dimensionality reduction name and and therefore needs to be set manually.
Author(s)
Maintainer: Samuel Marsh samuel.marsh@childrens.harvard.edu (ORCID)
Other contributors:
Ming Tang tangming2005@gmail.com [contributor]
Velina Kozareva [contributor]
Lucas Graybuck lucasg@alleninstitute.org [contributor]
See Also
Useful links:
Report bugs at https://github.com/samuel-marsh/scCustomize/issues