Ploidy Distribution

Subclone/cell mean/median CNV ploidy distrbution density plot.

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

Over the past decade, the single cell DNA CNV calling algorithms usually model the relationship between sequenced read count and copy number employing Poisson distribution with mappability, GC content, scale factor as confounding factor.

In cancer datasets, the copy number of different regions may encounter dramatic gain or loss. For single-cell DNA cancer data, ploidy distribution can intuitively display the tumor intra-heterogeneity.

To address this concern, in scSVAS platform, we develop a readily available web interface "Ploidy Distribution'' for interactive and real-time visualization of ploidy density plot for scDNA-seq data.

"Ploidy Distribution'' enables users to create the ploidy density plot just in one simple step as follow:

• Open https://sc.deepomics.org/demo-project/analyses/ploidydistribution in Google browser, and upload cnv profile file `*cnv.csvand predefined meta file*_meta.csv`.
• Optional With cnv profile file *_cnv.csv and predefined meta file *_meta.csv as inputs, users may also run scSVAS to get the subclone cluster result in *_meta_scsvas.csv first.

Then, you may get a matrix of the ploidy density plot of scDNA-seq data. The columns will list all categorical meta labels available in uploaded file *_meta_scsvas.csv by default. The first row displays the ploidy distribution of total single cells, just like the way for bulk sequencing. The second line exhibits the ploidy distribution of all subgroups for specific categorical meta labels in an aggregate form. Then, the following rows will list the ploidy distribution of all available subsets individually. Users can decide to display or hide these meta labels and subsets in "Editor-Select categorical meta label''. Users can choose to set the ploidy unit as cell mean ploidy or bin ploidy in "Editor-Mode''. If the mouse hovers over the density plot, 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 two major types of component in the "Ploidy Distribution'' application and their tooltipping and highlighting interactions are as follows:
  • Distribution plot
    The tooltip will display the current ploidy value and the density of that ploidy.
  • Aggregate subgroup distribution plot
    The tooltip will display the current ploidy value and the density of that ploidy on each subgroups.

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
  

  • Mode
    Users can select to display "cell mean ploidy" or "bin ploidy" mode.
  • Get log10-scale of count?
    Users can choose whether applies log10-scale on density count.
  • Set total number of intervals (bins)
    Users can set the total number of bins, the bin is the block that you use to combine values before getting the frequency.
  • Only get the plot with 10+ data?
    Users can decide whether filter subgroup plot with less than 10 data points.
  • Distribution plot height
    Users can adjust the height of each distribution plot.
  • Distribution plot width
    Users can adjust the width of each distribution plot.
  • Maximum value of ploidy
    Users can adjust the maximum value of ploidy in x-axis.

• Select categorical meta label
  User can choose which categorical meta labels to display.

• Color Palettes
  Users can customize color palettes for available categorical meta labels.

Version

v1.0.0 (2020-12-16)

Developer

Mr. Chaohui Li (GitHub)

Designer

Dr. Lingxi Chen (GitHub)

Updates

v1.0.0

• full functions implemented.