This repository hosts the code to reproduce the analysis steps for all technologies across all indications, including the visualization code for creating Figure and Supplementary Figures in our manuscript, titled
Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity.
To start with replicating our result, clone the repository to your working directory.
git clone https://github.com/bdsc-tds/mosaic_pilot_study.gitThe computational environment can be recreated by installing the singularity container from the .def file.
singularity build --force --fakeroot /path/to/container/environment.sif /path/to/file/environment.defLaunch the container from your terminal.
singularity shell --bind /scratch,/users,/work /path/to/container/environment.sifThe folder structure of this repository is detailed as follow
CHUV
├── Chromium
├── Visium
├── GeoMx
└── Manuscript_Figure
├── Figure 1 - 6
└── SuppFig
The analysis for each technology should be run in sequential order based on the naming of files. For bash files, only scripts titled main_.sh should be submitted as jobs to high computing clusters.
For visualization, the following code links are mapped to the creation of each figure/supplement figure.
| Script | Figures |
|---|---|
| Data Characteristics (Code) | Fig. 1 |
| Visium GeoMx Deconvolution Specificity (Code) | Fig. 2 |
| Visium GeoMx Registration (Code) | Fig. 3 |
| Visium Annotation Gallery (Code) | Fig. 4 |
| Intra-patient heterogeneity in Visium (Code) | Fig. 5 |
| Inter-patient heterogeneity across all technologies (Code) | Fig. 6 |
| Script | Supplementary Figures |
|---|---|
| Data Characteristics (Code) | Fig. S1 |
| Chromium UMAP (Code) | Fig. S2 |
| Chromium Characteristics (Code) | Fig. S3 |
| Chromium Characteristics (Code) | Fig. S3 dotplot |
| GeoMx Descriptive (Code)) | Fig. S4 |
| Visium Sample Gallery (Code) | Fig. S5 |
| Visium Pathology Deconvolution Agreement (Code) | Fig. S6 |
| Visium GeoMx Immune Abundance (Code) | Fig. S7 a,b |
| Visium Chromium Intra-patient heterogeneity (Code) | Figs. S7 c-g |
| Visium Integrated Annotation (Code) | Fig. S8 |
| Visium Ridge Plot (Code) | Fig. S9 a,b |
| GeoMx Ridge Plot (Code) | Fig. S9 c,d |
| Decon Assisted Inter-patient heterogeneity across all technologies (Code) | Fig. S9 e |