compare clusters

At a glance

Repository: atlasxomics/combined_cluster_wf · Display name: compare clusters · Modality: Epigenomics · Stage: Advanced Analysis

Overview

compare clusters explores differences in genes, peaks, and motifs between two user-defined cluster / condition groupings (GroupA vs GroupB) within an ArchRProject. It runs differential testing with ArchR::getMarkerFeatures and returns ranked tables and plots for each feature type.

Steps

1. compare_task — Assigns cells to GroupA / GroupB per the grouping specification, then runs pairwise differential testing across genes, peaks, and motifs and generates the plots and tables below. The closest option makes comparisons reciprocal (each group matched to its closest counterpart); use_max_possible_cells / max_cells bound the cells per group.

Inputs

Parameter	Type	Description
project_name	str	Name / identifier for the comparison; used in output paths.
archrproject	LatchDir	ArchRProject folder to analyze.
groupings	Manual | Barcodes | File	How to define GroupA / GroupB (see below).
use_max_possible_cells	bool	Use the largest possible number of cells per group (ignores max_cells).
max_cells	int	Upper bound on cells per comparison group (default 500).
closest	bool	Make pairwise results reciprocal (default True).

The groupings parameter is a union — pick one of three ways to define the two groups:

Mode	Fields	Use when
Manual (Groupings)	clusterA / conditionA / sampleA (+ multipleA) and the matching …B fields	You want to select each group by cluster, condition, and/or sample name. multipleA/B allow multiple values; cluster ranges like C5-C7 are expanded.
Barcodes (Barcodes)	groupA, groupB	You have explicit barcode lists for each group.
File (LatchFile)	an uploaded file	The group assignments are specified in a file.

Outputs

Written to latch:///compare_outs/<project_name>/.

compare_outs/<project_name>/
├── UpdateClustName_by_barcode.csv
├── all_genes.csv, marker_genes.csv, volcano_gene.pdf        # genes
├── all_peaks.csv, MA_peaks.pdf                              # peaks
└── all_motifs.csv, marker_motifs.csv,                       # motifs
    up/downRegulated_motifs.csv, up/downRegulated_motif_enrichment.pdf,
    volcano_motif.pdf

File	Description
UpdateClustName_by_barcode.csv	The selected cell barcodes and their assigned group (GroupA / GroupB).

Genes

File	Description
all_genes.csv	Full getMarkerFeatures differential-test results for every gene.
marker_genes.csv	Filtered / significance-scored markers (the volcano-plot source).
volcano_gene.pdf	Volcano plot of differential gene accessibility.

Peaks

File	Description
all_peaks.csv	Full differential-test results for every peak.
MA_peaks.pdf	MA plot of differential peaks.

Motifs

File	Description
all_motifs.csv	Full differential-test results for every motif.
marker_motifs.csv	Filtered / significance-scored motif markers (volcano source).
upRegulated_motifs.csv / downRegulated_motifs.csv	Up- and down-regulated motifs ranked by significance.
upRegulated_motif_enrichment.pdf / downRegulated_motif_enrichment.pdf	Enrichment plots of motifs ranked by −log10(FDR).
volcano_motif.pdf	Volcano plot of differential motif enrichment.

Example run

(Representative LaunchPlan / batch-table example to be added.)