Project abstract

This is a web application to visualize chromatin traces and provide interactive features which can be accessed at https://faryabilab.github.io/chromatin-traces-vis/

🚀 Getting Started

What You Can Do

• View and browse your chromatin traces as 3D models
• Inspect the distance between readouts easily
• Inspect the perimeter of any three readouts
• Filter linkage with a given distance threshold
• Distance heatmap
• Distance to the geometric center
• Radius of Gyration

📁 Supported File Types

Input Formats

Please ensure your CSV file contains the following required columns (case-insensitive):

• Either fov, s, readout, x, y, z
• Or fov, trace, readout, x, y, z

extra columns are ignored

Sample Data

Click to download an example CSV file: sample.csv

Sample data details

The sample dataset include three field of views (FOV):

• FOV1: one allele with no missing values
• FOV2: five alleles with no missing values
• FOV3: one allele WITH missing values

Data pre-process

This program is using linear interpolation to impute the missing values. When the interpolation switch is off by default, the missing readouts are colored gray on the model and the distance heatmap.

📋 How to Use

Step 1: Upload Your CSV File (Your file WILL NOT be saved to our database)

1. Click the button to start uploading.

2. Enter the number of Total Readouts. This step is required in order to fill in all the missing values. All the alleles will have this number of total readouts. You can enter other genomics infomation to display them on the distance map.

3. Drop your CSV file or click to upload. Your file WILL NOT be saved to our database.

4. Click the button to view your traces.

OR: Browse the files stored in our database

1. Use the shortcuts to view available chromatin traces.

2. Please submit your metadata and contact information through the form. Our team will reach out regarding data transfer and curation.

3. Keyword is pre-set for your convenience. You can clear the search bar to view the whole database.

4. Use column filter.

5. Inspect metadata.

6. Click view.

Step 2: Visualization Analysis

Basic

1. Select FOV and Allele to view any trace.

2. Use GUI to adjust

   1. Color
   2. Toggle Grid and axis
   3. Line Size
   4. Dot Size
   5. Toggle the distance label of a selected linkage
   6. Click Reset to clear all the selection of the dots.

Distance Analysis

1. Select any of the three options.
2. Filter readouts within a radius.
3. Calculate pairwise distance
   1. Click any two dots to view the distance.
   2. Filter alleles within the current fov with a maximum distance between two selected readouts.
4. Calculate 3-way perimeter.

Distance Heatmap

1. Click any grid cell to view the linkage in the 3D model.

2. Use the filter to filter the linkage distances that are within the range.

Centrality Profile

1. Hover to view the distance to the geometric center.

2. Click to download PDF

Radius of Gyration

1. Radius of Gyration.

Population Average Distance Map

A median distance map is calculated using non-interpolated data for all the alleles in all the FOV.