Cell Phylogeny

Top-down and circular zoomable cell phylogeny tree with cell-meta and cell-gene annotation.

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 build a readily available web interface "CNV Cell Phylogeny'' for interactive and real-time visualization of scDNA-seq data.

"CNV Cell Phylogeny'' enables users to create the cell phylogeny plot in one straightforward step as follow:

• With cnv profile file *_cnv.csv, predefined meta file *_meta.csv and targeted gene list as inputs, run scSVAS to get the single cells cutted dendrogram *_cut.json, the subclone and embedding results *_meta_scsvas.csv, and targeted gene cnv profiles *_gene_cnv.csv}.
• Open https://sc.deepomics.org/demo-project/analyses/cellphylogeny in Google browser, and upload files `*cut.json, optional filesmetascsvas.csvandgenecnv.csv`.

Then, you may get a cutted dendrogram of single cells. Users can switch the tree between "Topdown'' and "Circular'' modes. If the optional file *_meta.csv and *_gene_cnv.csv are uploaded, the cell meta and CNV heatmap will be shown. Users can decide to display or hide these meta labels in "Editor-Select categorical meta label''. If the mouse hovers over a dendrogram or heatmap, 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 "CNV View'' application and their tooltipping and highlighting interactions are as follows:
  • Cutted Dendrogram Node, Cutted Dendrogram Branch, Dendrogram Zooming, Meta CNV Heatmap
    Tooltipping and highlighting interactions are the same with "CNV View'' visualization.
  • Cell CNV Heatmap
    The tooltip will display the column name of a unit (such as gene or bin region) and its corresponding leaf node in the cutted dendrogram. Further, the column name, the leaf node, and the range of the leaf node will be highlighted.
• TopDown <=> Circular
  Users can click this button to switch the cutted dendrogram between "TopDown'' and "Circular'' modes.

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
  
  • Type of cutted dendrogram
    Users can choose the type of cutted dendrogram between "topdown'' and "circular''.
  • NA cases (seperated by comma ,)
    User can define the NA cases in CNV csv file, the default "N/A,NA'' means empty space "'', string "N/A", and string "NA" will be considered NA cases by file parser.
• Topdown Layout Settings
  Topdown Layout Settings are the same with "Layout Settings'' in "CNV Cell Phylogeny'' visualization.
• Circular Layout Settings
  
  • Basic
    
    • Figure margin - left
      Users can adjust the left margin of the figure.
    • Figure margin - top
      Users can adjust the top margin of the figure.
      
    • Margin between circular cutted dendrogram and meta heatmap
      Users can adjust the margin between circular cutted dendrogam and meta heatmap.
  • Circular Layout
    
    • Start angle of circular cutted dendrogam
      Users can adjust the start angle of circular cutted dendrogram.
    • End angle of circular cutted dendrogam
      Users can adjust the end angle of circular cutted dendrogram.
    • Inner radius of circular cutted dendrogram
      Users can adjust the inner radius of circular cutted dendrogram.
    • Unit width of CNV heatmap (integer recommended)
      Users can adjust the unit width of CNV and meta heatmap. Unit refers to the smallest rendered SVGobject in heatmap. Please note that the heatmap unit width are recommend to set as integer, floating point will make heatmap transparent owing to subpixel rendering.
• Color Palettes
  Users can customize color palettes for available categorical meta labels and continuous meta labels.

Version

v1.0.0 (2020-12-16)

Developer

Mr. Yuhao Qing (GitHub)

Mr. Lirui Kang (GitHub)

Designer

Dr. Lingxi Chen (GitHub)

Updates

v1.0.0

• full functionalities implemented.