Transcriptome Plots

At a glance

Repository: atlasxomics/plots_wt · Display name: Transcriptome Plots · Modality: Whole Transcriptome · Stage: Plots

Overview

Transcriptome Plots is an interactive Latch Plots notebook — an omic-agnostic AnnData viewer for spatial RNA-seq results. Each notebook runs on its own cloud VM and is driven through a GUI in console.latch.bio; the interface is 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

Transcriptome Plots loads a single AnnData .h5ad — the reduced combined_sm.h5ad produced by optimize_wt. It uses the sample, condition, and cluster obs columns as defaults when present (they're optional). optimize_wt also emits a Launch_Plots/artifact.json that opens its result directly in this Plots template.

Reduced object

combined_sm.h5ad is the visualization-optimized object: .X holds the log1p-normalized matrix (float32, sparse) and raw counts are kept in layers["counts"], but the PCA / neighbor graphs and most QC metadata are stripped. It's the right input for Plots; for re-clustering or anything needing what was dropped, use the full combined.h5ad — see the note on the optimize_wt page.

Starting Plots

1. Launch from the Workflow output (recommended). optimize_wt writes one folder per parameter set, each with its own artifact — so first pick a set from the top-level all_umaps.html / all_spatialdim.html galleries. Then in Latch Data open that set's folder under rna_analysis/<project>/ (e.g. set1_backend-scanpy_cr1-0-nc30-nn15-md0-5-sp1-0/) and use its Launch_Plots/artifact.json / Open in Plots action to start a notebook pre-loaded with that set's data.
2. Open Plots and select data manually. Start a new notebook from the Plots module in the Latch Console, then use the Select Data tab to point it at the chosen set's combined_sm.h5ad. Setting a data path (re)initializes every other tab.

Plotting modules

Each module is a tab in the Plots GUI.

Module	What it does
Welcome	Landing tab and report intro, plus the H5 Viewer for browsing the loaded AnnData — spatial and UMAP views, coloring by gene, and layout controls.
Select Data	Points the notebook at the .h5ad (the optimize_wt combined_sm.h5ad); specifying the path (re)initializes all other tabs.
Heatmap	Gene-expression heatmaps across clusters or groups.
Violin Plots	Distribution of a gene's expression across clusters or groups.
Proportion Plot	Cluster / condition composition — the proportion of cells per cluster across samples or conditions.

Other modalities

The epigenomics and co-profiling paths have their own Plots apps — Epigenomics Plots and Co-Profiling Plots.