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Co-Profiling Plots

At a glance

Repository: atlasxomics/plots_copro · Display name: Co-Profiling Plots · Modality: Co-Profiling · Stage: Plots

Overview

Co-Profiling Plots — the Spatial Single-Cell Co-Profiling Report — is an interactive Latch Plots notebook for jointly exploring the integrated epigenome × transcriptome result. Each notebook runs on its own cloud VM and is driven through a GUI in console.latch.bio, organized into tabs (each tab is a module).

Full walkthrough

For a click-through walkthrough of launching and using Plots, see the AtlasXPlots Tutorial.

How Plots connects to secondary analysis

Co-Profiling Plots loads an atx_glue output folder, which contains the SpatialGlue-integrated objects:

  • rna_copro_sm.h5ad — reduced transcriptome AnnData;
  • atac_gs_copro_sm.h5ad — reduced ATAC gene-score AnnData;
  • (the full rna_copro.h5ad / atac_gs_copro.h5ad are used as a fallback);
  • a coverages/ subdirectory of BigWig tracks;
  • a peak2gene/ subdirectory of peak-to-gene links.

The viewer lets you toggle between the two SpatialGlue modalities (RNA and ATAC gene score) and color by shared features.

Starting Plots

  1. Open Plots and select the glue output (recommended). Start a notebook from the Plots module in the Latch Console, then use the Select Data tab's folder picker to choose the atx_glue output directory (copro_integration_analysis/<project>/). The notebook loads the *_copro_sm.h5ad objects, coverages/, and peak2gene/, then (re)initializes every other tab.
  2. Launch from the Workflow output. If a Launch_Plots/artifact.json is present in the atx_glue output, use its Open in Plots action to start pre-loaded.

Plotting modules

Each module is a tab in the Plots GUI.

Module What it does
Welcome Landing tab and the Co-Profiling Report intro, plus the H5 Viewer — browse the loaded AnnData, toggle between the RNA and ATAC gene-score modalities, and color by features.
Select Data Points the notebook at an atx_glue output folder (the *_copro_sm.h5ad objects, coverages/, and peak2gene/); (re)initializes all other tabs.
GE H5 Viewer Gene-expression / ATAC gene-score H5 viewer; can save ATAC H5 data back to Latch Data.
Heatmap Feature heatmaps across clusters or groups.
Proportion Plot Cluster / condition composition across samples or conditions.
Track Browser Genome-browser view of coverage BigWig tracks from the coverages/ folder.
UMI Barplot UMI counts per cluster / sample.

Other modalities

The epigenomics and transcriptome paths have their own Plots apps — Epigenomics Plots and Transcriptome Plots.