Space Lineage

A visualization of clonal evolution history across multiple lesion with zoomable human anatomy altas.

For quick view of visualization application, please try the demo files in the "Editor" sidebar Demo File Sets. Description of demo files is available in demo data.

The uploaded input file must match the required format, please check the general accepted input file format.

Introduction

In scSVAS platform, we develop a readily available web interface "Space Lineage" for interactive and real-time visualization of clonal dynamics across multiple samples.

"Space Lineage'' enables users to create the clonal dynamics visualization just in following steps:

• Open https://sc.deepomics.org/demo-project/analyses/spaceprevalence in Google browser, and upload filessubclone tree file `clonaledges.csv, clonal prevelance fileclonal_prev.csv`.
• Optional With subclone tree file clonal_edges.csv and clonal prevelance file clonal_prev.csv as input, run scSVAS space.py to get the space tree results space_edges.csv, then upload it.
• Optional Users can also upload customized lesion images.

"Space Lineage" displays the clonal dynamics across subclones and lesions. If the mouse hovers over the node in lineage tree, an interactive tooltip carried its vital information will appear.

Interactions

• Download
  An SVG file will be generated when you click the "Download'' button. We offer two themes, dark and light. To switch to the light theme, please click the "Light Theme'' button.
• Tooltips and Highlights
  When your cursor hovers over an component on the visualization panel, essential information about the component will show up in the tooltip, and related components will be highlighted. There are several major types of component in the "Space Prevalence'' application and their tooltipping and highlighting interactions are as follows:
  • Subclone lineage tree node
    The tooltip will display the name of subclone/lesion, the clone prevalence at each timepoint if available. The corresponding subclone/lesion in lineage tree, fishplot will be highlighted.
  • Lesion lineage tree node
    The tooltip will display the lesion node name, distance to the root node, clonal frequency, the number of cells in the subclone. The corresponding lesion in other lineage tree will be highlighted.
  • Lesion lineage tree branch
    The tooltip will display the parent node name, child node name, and the distance of branch. The corresponding branch and nodes will be highlighted in other lineage tree.
• Anatomy image pointer
  For each lesion, we provide an image pointer. Users can right click the image pointer to active and deactive it. When the image pointer is activated, user can drag the pointer to anywhere they want in the anatomy image.

Editor Functionalities

The editor offers various options to fine-tune the visualization. Users can adjust the editor width and font size in "Editor Settings''.

• Demo File Sets, Files
  Demo file sets and files Functionalities are the same with "CNV View'' visualization.
• General Settings
  • Lineage Tree
    • Show subclone name
      Users can decide show clone name or not.
      
    • Type of lineage tree
      Users can change the type of lineage tree.
    • Show low prevelance clone
      Users can decide whether to show low prevalence clone or not.
    • Low prevalence threshold
      Users can change the value of low prevalence threshold, default it 0.01.
• Antomy type
  Users can select different antomy images.

Version

v1.0.0 (2020-12-19)

Developer

Dr. Lingxi Chen (GitHub)

Designer

Dr. Lingxi Chen (GitHub)

Acknowledgement

The anatomy images are designed by Freepik and macrovector / Freepik, we acknowledge for the free license.

Updates

v1.0.0

• full functionalities implemented.