# Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

## Documentation for package ‘scCustomize’ version 3.3.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I J L M N P Q R S T U V W

## -- 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_MALAT1_Threshold | Add MALAT1 QC Threshold
Add_MALAT1_Threshold.Seurat | Add MALAT1 QC Threshold
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
Dataset_Size_LIGER | Check size of LIGER datasets
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 --

ElbowPlot_scCustom | ElbowPlot with modifications
Embeddings.liger | Extract matrix of embeddings
ensembl_exAM_list | Immediate Early Gene (IEG) gene lists
ensembl_hemo_id | Ensembl Hemo IDs
ensembl_ieg_list | Immediate Early Gene (IEG) gene lists
ensembl_lncRNA_id | Ensembl lncRNA IDs
ensembl_malat1_list | MALAT1 gene lists
ensembl_mito_id | Ensembl Mito IDs
ensembl_ribo_id | Ensembl Ribo IDs
exAM_gene_list | exAM gene lists
exAM_Scoring | Add exAM Gene List Module Scores
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

## -- G --

Get_Reference_LIGER | Get Reference Dataset

## -- H --

Hue_Pal | 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 --

lncRNA_gene_list | lncRNA gene list

## -- M --

MAD_Stats | Median Absolute Deviation Statistics
Map_New_Meta | Create new variable from categories in meta.data
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
Proportion_Plot_per_Sample | Cell Proportion Plot per Sample
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_Add_cNMF | Read and add results from cNMF
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
Read_Velocity | Load RNA Velocity results
Reduction_Loading_Present | Check if reduction loadings are present
ReFilter_SeuratObject | Re-filter Seurat object
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
Top_Genes_Factor.liger | Extract top loading genes for LIGER factor
Top_Genes_Factor.Seurat | 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