Visualization Tools for Gene Regulatory Network Analysis

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Documentation for package ‘SimiCviz’ version 0.99.2

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

Help Pages

.compute_cell_auc	Compute AUC for a single cell
.ensure_genes_x_cells_format	Validate expression matrix is in genes x cells format
AUCProcessor	Initialize AUCProcessor
AUCProcessor-class	AUCProcessor class
auc_list_to_df	Collect per-label AUC matrices using cell labels
calculate_activity_scores	Calculate activity scores from SimiCvizExperiment weights
calculate_dissimilarity	Calculate dissimilarity scores across phenotype labels
calculate_ecdf_auc	Calculate ECDF AUC
compute_auc	Compute activity scores for an object
compute_auc-method	Compute activity scores for all cells
export_SimiCviz_csv	Export SimiCvizExperiment tables to CSV
get_auc	Extract activity scores from an object
get_auc-method	Get computed activity scores
get_tf_network	Extract stacked TF-target weight matrix across labels
is.SimiCvizExperiment	Check if object is a SimiCvizExperiment
load_cell_labels	Load cell-to-label mapping
load_collected_auc	Load a collected AUC CSV into a data.frame
load_expression_matrix	Load expression matrix from various sources /file formats Allowed formats: • CSV file • h5ad file • rds file (Seurat or SingleCellExperiment object) • matrix or data.frame in R
load_from_csv	Create a SimiCvizExperiment from CSV files
load_SimiCPipeline	Create a SimiCvizExperiment from SimiCPipeline output path
plot_auc_cumulative	Plot AUC cumulative (ECDF) curves by label
plot_auc_distributions	Plot AUC density distributions by label
plot_auc_heatmap	Plot mean AUC heatmap by TF and label
plot_auc_summary_statistics	Plot AUC summary statistics
plot_dissimilarity_heatmap	Plot dissimilarity heatmap
plot_r2_distribution	Plot adjusted R² distributions
plot_target_weights	Plot weight barplots for target genes
plot_tf_network_heatmap	Plot heatmap of a TF regulatory network across phenotypes
plot_tf_weights	Plot weight barplots for transcription factors
read_auc_csv	Read SimiC-style AUC results from CSV (compatibility)
read_auc_pickle	Read SimiCPipeline output AUC matrices (pickle file)
read_pickle	Read pickle files
read_weights_csv	Read Long-style TF-target weights from CSV (compatibility)
read_weights_pickle	Read SimiCPipeline output weights (pickle file)
setCellLabels	Set or update cell-to-label mapping
setLabelNames	Set or update label names and colors
show-method	AUCProcessor class
show-method	SimiCvizExperiment class
SimiCvizExperiment	Construct a SimiCvizExperiment object
SimiCvizExperiment-class	SimiCvizExperiment class