Time Lineage

A visualization of clonal evolution history across time with fishplot, lineage tree, and cellular ensemble.

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

As previously mentioned, many studies have observed that intra-tumor heterogeneity (ITH) is one of the principal causes of cancer therapy-resistant, tumor recurrence, and deaths. Over the past decades, researchers are interested in studying the clonal dynamics from multiple timepoint. For example, the time lineage between subclones before and after therapeutic intervention.

Herein, in scSVAS platform, we develop a readily available web interface "Time Lineage" for interactive and real-time visualization of clonal lineage across time for scDNA-seq data.

"Time Lineage" enables users to create the time lineage visualization just in following steps:

• Open https://sc.deepomics.org/demo-project/analyses/timelineage in Google browser, and upload the customized clonal tree file `clonaledges.csvand clonal prevalence fileclonal_prev.csv`.

"Time Lineage" is composed of fishplot, lineage tree, and cellular ensemble. As previously mentioned, the lineage tree exhibits the evolutionary relationship between tumor subclones. Users can choose different tree shapes from "topdown normal", "circular normal", and "circular acute". Fishplot conceptually manifests the proportion of tumor subclones at different tumorigenesis stages along time. We use the bezier curve to fit the trend of subclones over time. Two distinct head shapes ("bullet" and "onion") are offered. The cellular ensemble is an abstract aesthetic presenting the tumor's cellular prevalence at a certain point in time. If the mouse hovers over the subclone in fishplot, lineage tree, and cellular ensemble, 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 a 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 "Time Lineage" application and their tooltipping and highlighting interactions are as follows:
  • Subclone in fishplot
    The tooltip will display the name of subclone, the clone prevalence at each timepoint. The corresponding subclone in fishplot and lineage tree will be highlighted.
  • Lineage tree node
    The tooltip will display the subclone node name, distance to the root node, clonal frequency, the number of cells in the subclone. The corresponding subclone in fishplot and cellular ensemble will be highlighted.
  • 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 fishplot and cellular ensemble.
  • Cellular ensemble
    The tooltip will display the name and prevalence of the clone. The corresponding clones will be highlighted in lineage tree and fishplot.

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
  • Fishplot
    • Show clone name
      Users can decide show clone name or not.
    • X-axis title of fishplot
      Users can change the title for x-axis, default is "Time Point".
    • Y-axis title of fishplot
      Users can change the title for y-axis, default is "Clonal Prevalence".
    • Vertical layout of subclones
      Users can select the vertical layout of subclones from "stack", "space", and "center".
    • Head shape of fishplot
      Users can select the shape of clone head from "bullet" or "onion".
    • Width of fishplot
      Users can set the width of fishplot.
    • Height of fishplot
      Users can set the height of fishplot.
  • Lineage Tree
    • Title of lineage tree
      Users can change the title for lineage tree. default is "Clonal Lineage Tree".
    • Type of lineage tree
      Users can change the type of lineage tree.
  • Cellular Ensemble
    • Number of cells
      Users can adjust the number of cells in cellular ensemble presentation.
    • Radius of cellular aggregation
      Users can adjust the radius of cellular ensemble presentation.
• Color Palettes
  Users can customize color palettes for subclones .

Version

v1.0.0 (2020-12-16)

Developer

Mr. Chaohui Li (GitHub)

Designer

Dr. Lingxi Chen (GitHub)

Updates

v1.0.0

• full functionalities implemented.