Package index • GLEAM

Input and data extraction

score_signature(): Canonical signature scoring interface
seurat_mode(): Check Seurat compatibility mode
extract_embedding(): Extract embedding matrix

Geneset management

get_geneset(): Get geneset collection
list_geneset_sources(): List geneset sources
search_geneset(): Search pathways in a geneset collection
as_geneset(): Coerce geneset input to named list
read_gmt(): Read GMT file
check_geneset(): Validate genesets by size
match_geneset(): Match genesets to expression genes

Scoring

aggregate_signature(): Canonical signature aggregation interface
list_scoring_methods(): List available scoring methods
compare_scoring_methods(): Compare multiple scoring methods
run_gleam(): End-to-end GLEAM workflow

Differential analysis

test_signature(): Canonical signature testing interface
test_signature_spatial(): Canonical spatial signature testing interface
test_signature_trajectory(): Canonical trajectory signature testing interface

Trajectory analysis

extract_pseudotime(): Extract pseudotime values
extract_lineage(): Extract lineage labels
as_trajectory_data(): Convert trajectory inputs to a unified data.frame
join_score_trajectory(): Join score matrix and trajectory metadata
map_scores_to_trajectory(): Map scores to trajectory table
plot_pseudotime_score(): Plot signature score over pseudotime
plot_trajectory_score(): Plot signature score on trajectory embedding

Spatial analysis

join_score_spatial(): Join score with spatial coordinates
plot_spatial_score(): Plot signature score on spatial coordinates
plot_spatial_compare(): Plot spatial comparison result
plot_spatial_multi(): Plot multiple signatures on spatial coordinates

Visualization

gleam_theme(): GLEAM plotting theme
apply_gleam_theme(): Apply GLEAM theme to a ggplot
plot_dot(): Dot plot of signature summaries
plot_dot_bar(): Dot + bar summary plot for signature groups
plot_violin(): Violin plot of signature scores
plot_split_violin(): Split violin plot for signature scores
plot_ridge(): Ridge plot for signature score distributions
plot_box(): Box plot of sample-level signature scores
plot_pseudobulk_box(): Pseudobulk boxplot for signature scores
plot_embedding_score(): Plot signature score on embedding coordinates
plot_heatmap(): Heatmap of aggregated signature scores
plot_volcano(): Volcano plot for differential signatures
plot_celltype_compare(): Plot celltype comparison result
plot_group_in_celltype(): Plot group comparison within a fixed celltype
get_palette(): Get palette colors
list_palettes(): List available GLEAM palettes
scale_gleam_color(): GLEAM color scale helper
scale_gleam_fill(): GLEAM fill scale helper

Export and method comparison

collect_scores(): Collect score objects from multiple methods
summarize_scores(): Summarize score table
pivot_scores_long(): Pivot score matrix to long format
export_scores(): Export score table

Example data

hallmark: Built-in hallmark-like gene sets
immune_small: Built-in immune-focused small gene sets
pbmc_medium_matrix: Medium PBMC expression matrix for realistic demos
pbmc_medium_meta: Medium PBMC metadata for realistic demos
pbmc_small: Small PBMC example dataset (legacy compatibility)
spatial_medium_coords: Medium spatial coordinates
spatial_medium_expr: Medium spatial expression matrix
spatial_medium_meta: Medium spatial metadata
toy_expr: Tiny toy expression dataset for tests