diff --git a/docs/docs/tutorial-basics/create-a-document.md b/docs/docs/tutorial-basics/create-a-document.md index ffddfa8..96876bb 100644 --- a/docs/docs/tutorial-basics/create-a-document.md +++ b/docs/docs/tutorial-basics/create-a-document.md @@ -2,56 +2,50 @@ sidebar_position: 2 --- -# Create a Document +# Computing the Mean Cell Shape -Documents are **groups of pages** connected through: +This guide will walk you through each step in the process, ensuring you get the most out of our tool. -- a **sidebar** -- **previous/next navigation** -- **versioning** +### 📜 Step-by-Step Walkthrough -## Create your first Doc +1. **Initialization and Sidebar Header**: + - The sidebar displays the header "STEP 2: Compute Mean Shape". -Create a Markdown file at `docs/hello.md`: +2. **Data Selection**: + - The app first checks if you have uploaded or selected a dataset. + - If not, a warning prompts you to upload or select data using the "Load Data" option. + - If data is already uploaded, the filename is displayed for confirmation. -```md title="docs/hello.md" -# Hello +3. **Step Zero - Data Uploading**: + - If you haven't uploaded your data, navigate to the "Load Data" page and follow the instructions to ensure proper formatting. -This is my **first Docusaurus document**! -``` +4. **Analyzing Cell Data**: + - The app provides preprocessing steps, including interpolation, duplicate removal, and quotienting, to prepare your data for analysis. -A new document is now available at [http://localhost:3000/docs/hello](http://localhost:3000/docs/hello). +5. **Sampling Points Selection**: + - Use the slider to select the number of sampling points, which are crucial for the shape analysis. The default is set to 150. -## Configure the Sidebar +6. **Data Preprocessing**: + - Your data undergoes preprocessing to convert it into a suitable format for analysis. -Docusaurus automatically **creates a sidebar** from the `docs` folder. +7. **Exploring the Geodesic Trajectory** (Optional): + - If you wish to explore the geodesic trajectory between two cell shapes, activate the "Explore Geodesic Trajectory" toggle in the sidebar. + - Choose the desired treatment and cell line for your analysis. + - Use the provided sliders to select cell indices. + - The geodesic trajectory between the two chosen cell shapes is then visualized in a series of plots. -Add metadata to customize the sidebar label and position: +8. **Compute Mean Shape**: + - Activate the "Compute Mean Shape" toggle in the sidebar to begin this analysis. + - The computed mean shape will be displayed, which is essentially an average representation of all the cell shapes in your dataset. + - Three plots provide visual insights: + - A plot showcasing the mean estimate. + - A combined plot illustrating individual cell shapes alongside the mean estimate. + - A global mean shape superimposed on the entire dataset of cells. -```md title="docs/hello.md" {1-4} ---- -sidebar_label: 'Hi!' -sidebar_position: 3 ---- +### 🚀 Usage Tips: + +- **Always Check Data**: Ensure you've uploaded the correct dataset before proceeding with the analysis. +- **Sampling Points**: Adjusting the number of sampling points can provide different levels of granularity in the analysis. However, higher values may increase computation time. +- **Geodesic Trajectory**: This visualization helps understand the transition between two cell shapes, useful for comparing different treatments or cell lines. -# Hello - -This is my **first Docusaurus document**! -``` - -It is also possible to create your sidebar explicitly in `sidebars.js`: - -```js title="sidebars.js" -module.exports = { - tutorialSidebar: [ - 'intro', - // highlight-next-line - 'hello', - { - type: 'category', - label: 'Tutorial', - items: ['tutorial-basics/create-a-document'], - }, - ], -}; -``` +🔍 **Note**: Proper data preparation and understanding of each step are key to extracting meaningful insights from your cell shape data. Happy Analyzing! 🎉