index.qmd

---
title: "mPFC-web"
author: ZhengHu
date: 2023.07.12
---


```{r}
#| echo: false
#| message: false
#| warning: false

library(vitessceR)
library(tidyverse)
library(SeuratDisk)

#Adult.Ex <- readRDS('data/Adult.Ex.rds')
```



## scRNAseq

```{r}
#| echo: false
#| message: false
#| warning: false

adata_url <- "https://huggingface.co/datasets/TigerZheng/PFCdata/resolve/main/Adult_Ex.zarr"
#adata_url <- "https://pfcweb.oss-rg-china-mainland.aliyuncs.com/Adult_Ex.zarr"
#adata_path <- "data/Adult_Ex.zarr"
vc <- VitessceConfig$new(schema_version = "1.0.0", name = "Adult_Ex config")
dataset <- vc$add_dataset(name = "Adult_Ex", uid = "Adult_Ex")

dataset <- dataset$add_object(AnnDataWrapper$new(
  #adata_path = adata_path,
  adata_url = adata_url,
  obs_feature_matrix_path = "X",
  obs_embedding_paths = c("obsm/X_umap"),
  obs_embedding_names = c("UMAP"),
  obs_set_paths = c("obs/SubType_Layer", "obs/SubType"),
  obs_set_names = c("SubType_Layer", "SubType")
))

scatterplot_umap <- vc$add_view(dataset, Component$SCATTERPLOT, mapping = "UMAP")
cell_sets <- vc$add_view(dataset, Component$CELL_SETS)
genes <- vc$add_view(dataset, Component$GENES)

vc$layout(
  hconcat(
    scatterplot_umap,
    vconcat(cell_sets, genes)
  ))
vc$widget(theme = "light")
```