Co-Profiling

Co-Profiling is an optional path that combines the secondary-analysis outputs of the epigenomic and whole-transcriptome paths into a single integrated analysis.

How the workflows fit together

flowchart LR
    OPT["optimize WT"] --> GLUE["ATX Glue"]
    PROJ["create ArchRProject or<br>ATX_snap"] --> GLUE
    GLUE --> COPRO["ATX CoPro Plots"]
    COPRO -.-> COPRO_ANALYSES["<b>interactive analysis</b><br>module scoring<br>annotation<br>omics comparison<br>track browser"]

    PROJ:::process
    OPT:::process
    GLUE:::process
    COPRO:::process
    COPRO_ANALYSES:::interactive
    classDef process stroke:#818cf8,fill:#eef2ff
    classDef decision stroke:#fb923c,fill:#fff7ed
    classDef interactive stroke:#4ade80,fill:#f0fdf4,stroke-dasharray: 5 5
    classDef startend stroke:#a78bfa,fill:#f5f3ff

Walking the flow:

1. Inputs from both paths. Co-Profiling begins where the two modality paths leave off — the epigenomic objects from create ArchRProject or ATX_snap, and the transcriptome AnnData from optimize_wt. Both must be run first.
2. Integrate. ATX Glue uses SpatialGlue to spatially align the two modalities and derive joint clusters, along with cross-modality analyses (coverage, correlation, and peak-to-gene links).
3. Visualize. The integrated result is explored in ATX CoPro Plots — interactive module scoring, annotation, omics comparison, and track browser.

Workflows

Workflow	Purpose
atx_glue	Integrate epigenome and transcriptome with SpatialGlue.
Co-Profiling Plots	Interactive visualization of integrated results.