SpatialCellViz

An R Shiny app for visualization of spatial single-cell data with cell masks

SpatialCellViz makes it easy to explore spatial single-cell data across an ROI (region of interest)

Features

• Visualize spatial single-cell data for a single ROI
• Visualize cell masks
• Overlay cell phenotype, biomarker expression, or cellular neighborhoods on spatial plots
• Explore biaxial plots of biomarkers and subset by phenotype

Inputs

SpatialCellViz accepts a CSV file containing single-cell data and its corresponding .tiff file (upload limit: 1 G)

Required Columns

Column	Required?	Description
phenotype	Yes	Cell Phenotype
cell_label	Yes	Unique identifier for each cell that matches its corresponding cell in .tiff file

Running With Docker

https://hub.docker.com/repository/docker/j0shkramer/spatialcellviz/tags

Running Locally

Requirements

• R version ≥ 4.5.3
• R packages:
  • shiny
  • shinymanager
  • sf
  • terra
  • tidyverse
  • data.table
  • tmap
  • plotly
  • leaflet
  • Polychrome
  • pals
  • tools

Install the required packages in R:

install.packages(c(
    "shiny", "shinymanager", "sf", "terra", "tidyverse", "data.table",
    "tmap", "plotly", "leaflet", "Polychrome", "pals"
))

1. Clone the repository

git clone https://github.com/j0shkramer-op/SpatialCellViz.git

2. Navigate to repository

cd SpatialCellViz

3. Launch the app

shiny::runApp()