Plotting Cell Differentiation Lineage with D3.js

Published Oct 15, 2025
Updated Nov 15, 2025
1 minutes read
Note

This old post is translated by AI.

To visualize cell differentiation lineage, I created an interactive visualization tool using D3.js with Gemini. Why doesn't something this useful exist in the world?

##Demo

You can view the interactive cell differentiation lineage visualization from the following link:

Open Cell Differentiation Lineage Visualization

##Main Features

  • Hierarchical Structure Display: Displays differentiation pathways from ES cells to various differentiated cells as a phylogenetic tree
  • Japanese/English Language Switch: Switch between Japanese and English display with a button click
  • Marker Gene Display: Displays important marker genes at each differentiation stage
  • Zoom/Pan Function: Zoom with mouse wheel, pan by dragging
  • Color-Coded Display: Distinguishes terminally differentiated cells (green) and intermediate progenitor cells (blue) by color

##Cell Types Visualized

###Endoderm Lineage

  • Hepatocyte
  • Beta Cell
  • Alveolar Cell
  • Enterocyte

###Mesoderm Lineage

  • Hematopoietic cells (T cells, macrophages, neutrophils, erythrocytes, etc.)
  • Cardiomyocyte
  • Skeletal Muscle
  • Podocyte

###Ectoderm Lineage

  • Neuron
  • Astrocyte
  • Oligodendrocyte
  • Photoreceptor
  • Epidermis

##Technology Stack

  • D3.js v7: Data visualization and SVG manipulation
  • JavaScript: Interaction processing
  • HTML5/CSS3: Layout and styling

##How to Use

  • Mouse wheel: Zoom in/out
  • Drag: Pan the view
  • Language switch button: Switch between Japanese and English

Please try the interactive visualization!