# Single-Cell Exploratory Compositional Data Analysis

## Documentation for package ‘scECODA’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

calculate_pseudobulk | Calculate Pseudobulk from Count Matrix
calc_anosim | Analysis of Similarities (ANOSIM) R score
calc_ari | Calculate Adjusted Rand Index (ARI)
calc_clr | Perform the Centered Log-Ratio (CLR) transformation.
calc_freq | Calculate relative frequencies (percentages) column-wise.
calc_modularity | Calculate Adjusted Modularity Score
calc_sil | Calculate Average Silhouette Width
compute_KNN_from_dist | Compute K-Nearest Neighbors (KNN) from Distance Matrix
compute_snn_graph | Compute Shared Nearest Neighbor (SNN) Graph
create_long_data | Reshapes ECODA data into a long format for plotting and analysis.
deseq2_normalize | DESeq2 Normalization of Pseudobulk Data
ecoda | Create an SummarizedExperiment object from various data types
ecoda_helper | Core constructor for SummarizedExperiment objects from count/frequency matrices
example_data | Example Data for scECODA
find_hvcs | Identifies and stores Highly Variable Cell Types (HVCs) in an SummarizedExperiment object.
get_celltype_counts | Get the cell type counts from a long data frame (e.g. seurat object metadata) where each cell is a row.
get_celltype_variances | Calculates the variance of cell types across samples.
get_ecoda_assay | Helper to get assay for ecoda SummarizedExperiment objects
get_hvcs | Selects Highly Variable Cell Types (HVCs) based on variance or count threshold.
get_sample_metadata | Extracts constant metadata for each sample from a cell-level data frame.
plot_barplot | Generates a Stacked Bar Plot of Cell Type Relative Abundance.
plot_boxplot | Generates Boxplots for CLR-transformed Cell Type Abundances with Optional Group Comparison.
plot_corr | Plot Cell Type Correlation Matrix
plot_heatmap | Generates a Heatmap of Cell Abundance Data from an SummarizedExperiment assay.
plot_pca | Plot Principal Component Analysis and Calculate Clustering Scores
plot_pca3d | Plot 3-dimensional interactive Principal Component Analysis plot
plot_varmean | Generates a Mean-Variance Plot for CLR-transformed Cell Type Data.
replace_zeros | Replace zero values in count or frequency data