# Cases on 10x Visium Data

Here we provide case applications based on 10x Visium data (which are not at single-cell resolution). For convenience, we used the `Quick Mode` here, but you can also follow the {doc}`Step by Step <step_by_step>` Guide to analyze 10x Visium data—the steps are the same.

A frequently asked question is how to provide annotations for 10x Visium data. Note that gsMap can run without annotations. The most convenient approaches are to either leave the `annotation` parameter unset (in {doc}`Step by Step <step_by_step>`) or provide annotations from spatial clustering methods, such as [SpaGCN](https://github.com/jianhuupenn/SpaGCN).

## Preparation

Make sure you have {doc}`installed <install>` the `gsMap` package before proceeding.

### 1. Download Dependencies

The `gsMap` package in quick mode requires the following resources:

- **Gene transfer format (GTF) file**, for gene coordinates on the genome.
- **LD reference panel**, in quick mode, we provide a pre-built LD score snp-by-gene matrix based on 1000G_EUR_Phase3.
- **SNP weight file**, to adjust correlations between SNP-trait association statistics.
- **Homologous gene transformations file** (optional), to map genes between species.

To download all the required files:

```bash
wget https://yanglab.westlake.edu.cn/data/gsMap/gsMap_resource.tar.gz
tar -xvzf gsMap_resource.tar.gz
```

Directory structure:

```bash
tree -L 2

gsMap_resource
    ├── genome_annotation
    │   ├── enhancer
    │   └── gtf
    ├── homologs
    │   ├── macaque_human_homologs.txt
    │   └── mouse_human_homologs.txt
    ├── LD_Reference_Panel
    │   └── 1000G_EUR_Phase3_plink
    ├── LDSC_resource
    │   ├── hapmap3_snps
    │   └── weights_hm3_no_hla
    └── quick_mode
        ├── baseline
        ├── SNP_gene_pair
        └── snp_gene_weight_matrix.h5ad
```

### 2. Download Example Data

You can download the example 10x Visium data as follows:

```bash
wget https://yanglab.westlake.edu.cn/data/gsMap/Visium_example_data.tar.gz
tar -xvzf Visium_example_data.tar.gz
```

Directory structure:

```bash
tree -L 2

Visium_example_data/
├── GWAS
│   ├── IQ_NG_2018.sumstats.gz
│   └── Serum_creatinine.sumstats.gz
└── ST
    ├── V1_Adult_Mouse_Brain_Coronal_Section.h5ad
    ├── V1_Mouse_Brain_Sagittal_Posterior_Section.h5ad
    └── V1_Mouse_Kidney.h5ad
```

## Case1

Data: Visium data of adult mouse coronal section
Trait: IQ
<span style="color:#31a354"> Required memory: 11G (2902 cells) </span>

```bash
gsmap quick_mode \
    --workdir './example_quick_mode/Visium' \
    --homolog_file 'gsMap_resource/homologs/mouse_human_homologs.txt' \
    --sample_name 'V1_Adult_Mouse_Brain_Coronal_Section' \
    --gsMap_resource_dir 'gsMap_resource' \
    --hdf5_path 'Visium_example_data/ST/V1_Adult_Mouse_Brain_Coronal_Section.h5ad' \
    --annotation 'domain' \
    --data_layer 'count' \
    --sumstats_file 'Visium_example_data/GWAS/IQ_NG_2018.sumstats.gz' \
    --trait_name 'IQ'
```

[gsMap report](https://yanglab.westlake.edu.cn/data/gsMap/Visium_report/coronal/V1_Adult_Mouse_Brain_Coronal_Section_IQ_gsMap_Report.html) for the `IQ` on the adult mouse coronal section Visium data.

## Case2

Data: Visium data of adult mouse sigital section
Trait: IQ

<span style="color:#31a354"> Required memory: 12G (3289 cells) </span>

```bash
gsmap quick_mode \
    --workdir './example_quick_mode/Visium' \
    --homolog_file 'gsMap_resource/homologs/mouse_human_homologs.txt' \
    --sample_name 'V1_Mouse_Brain_Sagittal_Posterior_Section' \
    --gsMap_resource_dir 'gsMap_resource' \
    --hdf5_path 'Visium_example_data/ST/V1_Mouse_Brain_Sagittal_Posterior_Section.h5ad' \
    --annotation 'domain' \
    --data_layer 'count' \
    --sumstats_file 'Visium_example_data/GWAS/IQ_NG_2018.sumstats.gz' \
    --trait_name 'IQ'
```

[gsMap report](https://yanglab.westlake.edu.cn/data/gsMap/Visium_report/saggital/V1_Mouse_Brain_Sagittal_Posterior_Section_IQ_gsMap_Report.html) for the `IQ` on the adult mouse sigital section Visium data.

## Case3

Data: Visium data of adult mouse kindey
Trait: Serum creatinine

<span style="color:#31a354"> Required memory: 8G (1437 cells) </span>

```bash
gsmap quick_mode \
    --workdir './example_quick_mode/Visium' \
    --homolog_file 'gsMap_resource/homologs/mouse_human_homologs.txt' \
    --sample_name 'V1_Mouse_Kidney' \
    --gsMap_resource_dir 'gsMap_resource' \
    --hdf5_path 'Visium_example_data/ST/V1_Mouse_Kidney.h5ad' \
    --annotation 'domain' \
    --data_layer 'count' \
    --sumstats_file 'Visium_example_data/GWAS/Serum_creatinine.sumstats.gz' \
    --trait_name 'Serum_creatinine'
```

[gsMap report](https://yanglab.westlake.edu.cn/data/gsMap/Visium/V1_Mouse_Kidney_Serum_creatinine_gsMap_Report.html) for the `Serum creatinine` on the adult mouse kindey Visium data.