This repo will cover all of the code linked to Castillo et al.
(Manuscript Title: Spatial transcriptomics stratifies health and psoriatic disease severity by emergent cellular ecosystems)
All of the raw files linked to this project can be found under GEO Accession number - (GSE202011)
Please make sure to install all of the dependencies prior to running the code. The following dependencies are essential:-
Seurat (Recommended V4)
Original manuscript was based on V3.2
Tidyverse
NicheNet
Harmony
SpaceFold (https://github.com/dpeerlab/SpaceFold)
BayesPrism (https://github.com/Danko-Lab/BayesPrism)
Original manuscript used TED, now archived at (https://github.com/Danko-Lab/TED)
DESeq2
ggsci (For color palettes only)
The code is organised into several R notebooks with each notebook covering different parts of the analysis. The figure numbers and references are found within each notebook and a table content will also be added to link each figure to different parts of code for ease of navigation. Reproducibility is the key here, please contact XXXX for any issues with the code.
The notebooks will also require you to import the data from the linked Zenodo / Figshare repository (Will be added soon) in order to reproduce all of the respective figures.
Each notebook link will take you to the notebook with necessary code, please select the figure number in the table of contents found on top of the notebook to .
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
1B | link | Spatial Plot - Healthy sample with cluster labels |
1C | link | UMAP (Healthy samples only) - with spatial regions labels |
1D | link | Percentage composition (Healthy samples only) |
1E | link | Seurat Integeration (scRNA + ST data) showing cell type enrichment |
1G | link | MIA - healthy skin with dataset 1 (Hughes et al.) - Structural cell types only |
1H | link | MIA - healthy skin with dataset 2 (Reynolds et al.) - Structural cell types only |
1I | link | MIA - healthy skin with dataset 3 (Sullivan et al.) - APCs and Preadiplocytes |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
2A | link | MIA - healthy skin with dataset 1 (Hughes et al.) - Immune cell types only |
2B | link | MIA - healthy skin with dataset 2 (Reynolds et al.) - Immune cell types only |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
3A | link | Spatial Plots with cluster labels - Lesional and Non-Lesional skin |
3B | link | UMAP - All samples combined (PS + Healthy skin) after Harmony batch correction |
3C | link | Percentage composition plots for different clusters / spatial regions |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
4E | link | Circos plot visualization - cluster 4 receptor with clusters 7, 3 and 10 as ligand. |
4F | link | Circos plot visualization - cluster 7 receptor with clusters 10, 3 and 4 as ligand. |
4G | link | Circos plot visualization - cluster 10 receptor with clusters 7, 3 and 4 as ligand. |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
5A | link | MIA for (PS only) dataset 1 - Immune cell types |
5B | link | MIA for (PS only) dataset 2 - Immune cell types |
5C | link | MIA for TRM (Tisssue resident memory cells) dataset |
5D | link | Space-fold projection - Healthy, non-lesional and lesional skin. |
5E | link | B cell (From dataset 1) pathways |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
6A | link | Hierarchical clustering based heatmap for all samples |
6B | link | PCA plot for all samples - grouped by PS group |
6C | link | PCA plot for all samples - grouped by Disease severity |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
7A | link | Space-fold projection - Mild disease (split into non-lesional and lesional) |
7B | link | Space-fold projection - Moderate-severe disease (split into non-lesional and lesional) |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
8A | link | PCA plot - Pseudobulk for cluster 1 (Derm macrophages, fibroblasts) |
8B | link | PCA plot - Pseudobulk for cluster 12 (Derm macrophages, fibroblasts) |
8E | link | Spatial Feature plots #1 |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S2-B | link | Spatial Plots (Before and after filtering) |
S2-C | link | Heat-map showing top 8 marker genes per cluster (Healthy sample data only) |
S2-D | link | UMI counts |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S3-A | link | Heatmap for Healthy samples - after Harmony batch correction |
S3-B | link | UMAP - Healthy skin after Harmony batch correction |
S3-C | link | Percentage composition plots for different clusters / spatial regions (Healthy skin) |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S4-A | link | UMAP - healthy skin with scRNA dataset 1 (Hughes et al.) |
S4-B | link | UMAP - healthy skin with scRNA dataset 2 (Reynolds et al.) |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S5-A | link (Anchor data UMAP) | UMAP plots - Harmony batch correction vs Anchor batch correction |
S5-A | link (Harmony data UMAP) | UMAP plots - Harmony batch correction vs Anchor batch correction |
S5-C | link (Anchor data) | Spatial plots- Harmony batch correction vs Anchor batch correction |
S5-C | link (Harmony data) | Spatial plots- Harmony batch correction vs Anchor batch correction |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S6 | link | Heat-map showing top 10 marker genes per cluster (All samples) - Harmony batch corrected |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S7 | link | Heat-map showing top 10 marker genes per cluster (All samples) - Anchor batch corrected |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S8-B | link | UMIs per clusters - Harmony batch corrected data |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S9-A | link | Seurat Integration (scRNA + ST data) showing cell type enrichment fpr psoriatic lesional skin ST |
S9-B | link | Psoriatic skin scRNA-seq dataset 1 |
S9-C | link | Psoriatic skin scRNA-seq dataset 2 |
S9-D | link | MIA - PS skin with dataset 1 (Hughes et al.) - Structural cell types only |
S9-E | link | MIA - PS skin with dataset 2 (Reynolds et al.) - Structural cell types only |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S10A | link | Dendogram for all samples based on pseudo-bulk expression |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S11 | link | PCA plots - per cluster basis (PS samples only) |
FIGURE NO | NOTEBOOK LINK | DESCRIPTION |
---|---|---|
S13 | link | Spatial Feature expression plots #2 |