Shiny Single Cell Browser

Interactive visualization of single cell RNAseq datasets.

• Visualize cluster distribution, marker gene expression levels.
• Select or click on a gene to show its expression on t-SNE/UMAP plots, select a cluster to show its marker genes.
• Specify pre-analyzed datasets (Seurat v2 or v3 format) in the JSON config file.

Published data using this web app:

• Human Organoid Single-Cell Browser -- Y Wang, et al. Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes, Nature Communications, 2022
• Human Testis Atlas Browser -- J Guo, et al. The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty, Cell Stem Cell, 2020
• Fluorescent cells isolated from Zebrafish Tg(olig2:dsred) - L Xing, et al. Expression of myelin transcription factor 1 and lamin B receptor mediate neural progenitor fate transition in the zebrafish spinal cord pMN domain, J. Biological Chemistry, 2022

Setting up the Single Cell Browser

• Download the source code -- git clone https://github.com/yueqiw/shiny_cell_browser.git.
• Install package dependencies listed in requirements.txt.
  • The app has been tested in R version 3.6.3.
  • Seurat v2.3.4 and v3.1.0 are supported. These versions can be installed following the official instructions.
• Prepare Seurat data
  • Analyze the dataset following Seurat v2 or v3 pipeline (clustering, t-SNE/UMAP, differential expression, etc). Alternatively, create a Seurat object by converting from other formats.
  • Store the Seurat v2 or v3 data object as a .rds file using saveRDS(). Place the .rds file in the data/ folder.
  • The Seurat data object (or the RNA assay in Seurat3) should fill the @data slot with the normalized and log-transformed gene expression matrix (ideally in a sparse dgCMatrix format to save space). The @raw.data and @scale.data slots are not used -- setting them to NULL may speed up the loading time.
  • The Seurat object should contain a 2D cell embedding created using t-SNE or UMAP.
  • The @meta.data table should use cell names as row names and contain a column that indicates the cluster id for each cell. Optionally, the display color of each cluster can be stored as a named vector in @misc. For examples, if the clusters are stored as [email protected]$my_clusters, their colors can be stored as seurat_data@misc$my_clusters_colors.
  • Store the marker gene differential expression table in a .csv file in the data/ folder. The table must contain two columns named gene and cluster. Other columns may have any name.
• Specify the visualization config and data file paths by creating a data/config.json file and following the example in data/example_config.json.
  • Multiple datasets can be configured in the same browser.
  • The browser-level config includes the browser title and url link
  • The dataset-level config options are listed below:
    • name: the dataset name.
    • file: the .rds file path.
    • cluster: the name of the column containing the displayed cluster ids.
    • embedding: the type of 2D embedding (e.g. tsne or umap).
    • diff_ex_cluster: the name of the @meta.data cluster id column that corresponds to the cluster ids in the differential expression csv file. In most cases, this is the same as cluster.
    • diff_ex_file: the marker gene differential expression csv file.
    • cluster_name_mapping (optional): a mapping from the Seurat cluster ids to more readable cluster names.
    • pt_size (optional): if set, overrides the automatically computed point size in embedding plots.
    • font_scale (optional): if set, scales the font size of cluster labels by this factor.
    • label_coordinates (optional): if set, the cluster labels will be placed at these coordinates rather than at the center of each cluster.

Launching the Single Cell Browser locally

• Set the working directory (e.g. cd shiny_cell_browser in command line, or setwd in Rstudio)
• Launch the Single Cell Browser locally. Run ./run_app.sh in the comand line, or shiny::runApp() in Rstudio.
• This should launch the browser on the local computer at http://127.0.0.1:4894/. The port number can be changed (e.g. shiny::runApp(port=1234)).
• For other computers in the local network to access the web app, specify host='0.0.0.0', port=1234 in the runApp call, then visit http://your-ip-address:1234.

Deploy the Single Cell Browser

• The App can be easily deployed on a web server using shinyapps.io, which supports both free and paid servers. Docker is an alternative approach but takes longer to set up.
• To set up a shinyapps.io account and learn how to deploy a Shiny app, follow this tutorial.
• After setting up the account, deploy the app by rsconnect::deployApp().

If you encounter the following error: Error parsing manifest: Unable to determine package source for Bioconductor package Biobase: Repository must be specified, run this before deployApp: options(repos = BiocManager::repositories()

Updates

see updates.md