Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Documentation for package ‘scCustomize’ version 3.0.0

Help Pages

-- A --

Add_Alt_Feature_ID	Add Alternative Feature IDs
Add_CellBender_Diff	Calculate and add differences post-cell bender analysis
Add_Cell_Complexity	Add Cell Complexity
Add_Cell_Complexity.liger	Add Cell Complexity
Add_Cell_Complexity.Seurat	Add Cell Complexity
Add_Cell_QC_Metrics	Add Multiple Cell Quality Control Values with Single Function
Add_Cell_QC_Metrics.liger	Add Multiple Cell Quality Control Values with Single Function
Add_Cell_QC_Metrics.Seurat	Add Multiple Cell Quality Control Values with Single Function
Add_Hemo	Add Hemoglobin percentages
Add_Hemo.liger	Add Hemoglobin percentages
Add_Hemo.Seurat	Add Hemoglobin percentages
Add_Mito_Ribo	Add Mito and Ribo percentages
Add_Mito_Ribo.liger	Add Mito and Ribo percentages
Add_Mito_Ribo.Seurat	Add Mito and Ribo percentages
Add_Pct_Diff	Add percentage difference to DE results
Add_Sample_Meta	Add Sample Level Meta Data
Add_Top_Gene_Pct	Add Percent of High Abundance Genes
Add_Top_Gene_Pct.liger	Add Percent of High Abundance Genes
Add_Top_Gene_Pct.Seurat	Add Percent of High Abundance Genes
as.anndata	Convert objects to anndata objects
as.anndata.liger	Convert objects to anndata objects
as.anndata.Seurat	Convert objects to anndata objects
as.LIGER	Convert objects to LIGER objects
as.LIGER.list	Convert objects to LIGER objects
as.LIGER.Seurat	Convert objects to LIGER objects
as.Seurat.liger	Convert objects to 'Seurat' objects

-- B --

Barcode_Plot	Create Barcode Rank Plot
Blank_Theme	Blank Theme

-- C --

Case_Check	Check for alternate case features
CellBender_Diff_Plot	Plot Number of Cells/Nuclei per Sample
CellBender_Feature_Diff	CellBender Feature Differences
Cells.liger	Extract Cells from LIGER Object
Cells_by_Identities_LIGER	Extract Cells by identity
Cells_per_Sample	Cells per Sample
Cell_Highlight_Plot	Meta Highlight Plot
Change_Delim_All	Change all delimiters in cell name
Change_Delim_Prefix	Change barcode prefix delimiter
Change_Delim_Suffix	Change barcode suffix delimiter
CheckMatrix_scCustom	Check Matrix Validity
Clustered_DotPlot	Clustered DotPlot
Cluster_Highlight_Plot	Cluster Highlight Plot
Cluster_Stats_All_Samples	Calculate Cluster Stats
ColorBlind_Pal	Color Universal Design Short Palette
Convert_Assay	Convert between Seurat Assay types
Copy_From_GCP	Copy folder from GCP bucket from R Console
Copy_To_GCP	Copy folder to GCP bucket from R Console
Create_10X_H5	Create H5 from 10X Outputs
Create_CellBender_Merged_Seurat	Create Seurat Object with Cell Bender and Raw data
Create_Cluster_Annotation_File	Create cluster annotation csv file

-- D --

Dark2_Pal	Dark2 Palette
DimPlot_All_Samples	DimPlot by Meta Data Column
DimPlot_LIGER	DimPlot LIGER Version
DimPlot_scCustom	DimPlot with modified default settings
DiscretePalette_scCustomize	Discrete color palettes
DotPlot_scCustom	Customized DotPlot

-- E --

Embeddings.liger	Extract matrix of embeddings
ensembl_hemo_id	Ensembl Hemo IDs
ensembl_ieg_list	Immediate Early Gene (IEG) gene lists
ensembl_mito_id	Ensembl Mito IDs
ensembl_ribo_id	Ensembl Ribo IDs
Extract_Modality	Extract multi-modal data into list by modality
Extract_Sample_Meta	Extract sample level meta.data
Extract_Top_Markers	Extract Top N Marker Genes

-- F --

Factor_Cor_Plot	Factor Correlation Plot
FeaturePlot_DualAssay	Customize FeaturePlot of two assays
FeaturePlot_scCustom	Customize FeaturePlot
Features.liger	Extract Features from LIGER Object
FeatureScatter_scCustom	Modified version of FeatureScatter
Feature_Present	Check if genes/features are present
Fetch_Meta	Get meta data from object
Fetch_Meta.liger	Get meta data from object
Fetch_Meta.Seurat	Get meta data from object
Find_Factor_Cor	Find Factor Correlations

-- H --

Hue_Pal

-- I --

Idents.liger	Extract or set default identities from object
Idents<-.liger	Extract or set default identities from object
ieg_gene_list	Immediate Early Gene (IEG) gene lists
Iterate_Barcode_Rank_Plot	Iterative Barcode Rank Plots
Iterate_Cluster_Highlight_Plot	Iterate Cluster Highlight Plot
Iterate_DimPlot_bySample	Iterate DimPlot By Sample
Iterate_FeaturePlot_scCustom	Iterative Plotting of Gene Lists using Custom FeaturePlots
Iterate_Meta_Highlight_Plot	Iterate Meta Highlight Plot
Iterate_PC_Loading_Plots	Iterate PC Loading Plots
Iterate_Plot_Density_Custom	Iterative Plotting of Gene Lists using Custom Density Plots
Iterate_Plot_Density_Joint	Iterative Plotting of Gene Lists using Custom Joint Density Plots
Iterate_VlnPlot_scCustom	Iterative Plotting of Gene Lists using VlnPlot_scCustom

-- J --

JCO_Four

Four Color Palette (JCO)

-- L --

Liger_to_Seurat

Create a Seurat object containing the data from a liger object *[Soft-deprecated]*

-- M --

MAD_Stats	Median Absolute Deviation Statistics
Median_Stats	Median Statistics
Merge_Seurat_List	Merge a list of Seurat Objects
Merge_Sparse_Data_All	Merge a list of Sparse Matrices
Merge_Sparse_Multimodal_All	Merge a list of Sparse Matrices contain multi-modal data.
Meta_Highlight_Plot	Meta Highlight Plot
Meta_Numeric	Check if meta data columns are numeric
Meta_Present	Check if meta data are present
Meta_Remove_Seurat	Remove meta data columns containing Seurat Defaults
Move_Legend	Move Legend Position
msigdb_qc_ensembl_list	QC Gene Lists
msigdb_qc_gene_list	QC Gene Lists

-- N --

NavyAndOrange

Navy and Orange Dual Color Palette

-- P --

PalettePlot	Plot color palette in viewer
PC_Plotting	PC Plots
Percent_Expressing	Calculate percent of expressing cells
plotFactors_scCustom	Customized version of plotFactors
Plot_Cells_per_Sample	Plot Number of Cells/Nuclei per Sample
Plot_Density_Custom	Nebulosa Density Plot
Plot_Density_Joint_Only	Nebulosa Joint Density Plot
Plot_Median_Genes	Plot Median Genes per Cell per Sample
Plot_Median_Mito	Plot Median Percent Mito per Cell per Sample
Plot_Median_Other	Plot Median other variable per Cell per Sample
Plot_Median_UMIs	Plot Median UMIs per Cell per Sample
Proportion_Plot	Cell Proportion Plot
Pull_Cluster_Annotation	Pull cluster information from annotation csv file.
Pull_Directory_List	Pull Directory List

-- Q --

QC_Histogram	QC Histogram Plots
QC_Plots_Combined_Vln	QC Plots Genes, UMIs, & % Mito
QC_Plots_Complexity	QC Plots Cell "Complexity"
QC_Plots_Feature	QC Plots Feature
QC_Plots_Genes	QC Plots Genes
QC_Plots_Mito	QC Plots Mito
QC_Plots_UMIs	QC Plots UMIs
QC_Plot_GenevsFeature	QC Plots Genes vs Misc
QC_Plot_UMIvsFeature	QC Plots UMI vs Misc
QC_Plot_UMIvsGene	QC Plots Genes vs UMIs

-- R --

Random_Cells_Downsample	Randomly downsample by identity
Read10X_GEO	Load in NCBI GEO data from 10X
Read10X_h5_GEO	Load in NCBI GEO data from 10X in HDF5 file format
Read10X_h5_Multi_Directory	Load 10X h5 count matrices from multiple directories
Read10X_Multi_Directory	Load 10X count matrices from multiple directories
Read_CellBender_h5_Mat	Load CellBender h5 matrices (corrected)
Read_CellBender_h5_Multi_Directory	Load CellBender h5 matrices (corrected) from multiple directories
Read_CellBender_h5_Multi_File	Load CellBender h5 matrices (corrected) from multiple files
Read_GEO_Delim	Load in NCBI GEO data formatted as single file per sample
Read_Metrics_10X	Read Overall Statistics from 10X Cell Ranger Count
Read_Metrics_CellBender	Read Overall Statistics from CellBender
Reduction_Loading_Present	Check if reduction loadings are present
Rename_Clusters	Rename Clusters
Rename_Clusters.liger	Rename Clusters
Rename_Clusters.Seurat	Rename Clusters
Replace_Suffix	Replace barcode suffixes

-- S --

scCustomize_Palette	Color Palette Selection for scCustomize
Seq_QC_Plot_Alignment_Combined	QC Plots Sequencing metrics (Alignment) (Layout)
Seq_QC_Plot_Antisense	QC Plots Sequencing metrics (Alignment)
Seq_QC_Plot_Basic_Combined	QC Plots Sequencing metrics (Layout)
Seq_QC_Plot_Exonic	QC Plots Sequencing metrics (Alignment)
Seq_QC_Plot_Genes	QC Plots Sequencing metrics
Seq_QC_Plot_Genome	QC Plots Sequencing metrics (Alignment)
Seq_QC_Plot_Intergenic	QC Plots Sequencing metrics (Alignment)
Seq_QC_Plot_Intronic	QC Plots Sequencing metrics (Alignment)
Seq_QC_Plot_Number_Cells	QC Plots Sequencing metrics
Seq_QC_Plot_Reads_in_Cells	QC Plots Sequencing metrics
Seq_QC_Plot_Reads_per_Cell	QC Plots Sequencing metrics
Seq_QC_Plot_Saturation	QC Plots Sequencing metrics
Seq_QC_Plot_Total_Genes	QC Plots Sequencing metrics
Seq_QC_Plot_Transcriptome	QC Plots Sequencing metrics (Alignment)
Seq_QC_Plot_UMIs	QC Plots Sequencing metrics
seq_zeros	Create sequence with zeros
Setup_scRNAseq_Project	Setup project directory structure
Single_Color_Palette	Single Color Palettes for Plotting
SpatialDimPlot_scCustom	SpatialDimPlot with modified default settings
Split_Layers	Split Seurat object into layers
Split_Vector	Split vector into list
Stacked_VlnPlot	Stacked Violin Plot
Store_Misc_Info_Seurat	Store misc data in Seurat object
Store_Palette_Seurat	Store color palette in Seurat object
Subset_LIGER	Subset LIGER object

-- T --

theme_ggprism_mod	Modified ggprism theme
Top_Genes_Factor	Extract top loading genes for LIGER factor

-- U --

UnRotate_X	Unrotate x axis on VlnPlot
Updated_HGNC_Symbols	Update HGNC Gene Symbols
Updated_MGI_Symbols	Update MGI Gene Symbols

-- V --

VariableFeaturePlot_scCustom	Custom Labeled Variable Features Plot
Variable_Features_ALL_LIGER	Perform variable gene selection over whole dataset
viridis_dark_high	Viridis Shortcuts
viridis_inferno_dark_high	Viridis Shortcuts
viridis_inferno_light_high	Viridis Shortcuts
viridis_light_high	Viridis Shortcuts
viridis_magma_dark_high	Viridis Shortcuts
viridis_magma_light_high	Viridis Shortcuts
viridis_plasma_dark_high	Viridis Shortcuts
viridis_plasma_light_high	Viridis Shortcuts
VlnPlot_scCustom	VlnPlot with modified default settings

-- W --

WhichCells.liger

Extract Cells for particular identity