Download and Check the official demo input.

Introduction

The 'Single Sample' visualization is an interactive version of the output plot from 'Patchwork', a bioinformatics tool for analyzing allele-specific copy numbers (CN) and loss-of-heterozygosity in cancer genomes. This visualization summarizes all 24 chromosomal plots generated by 'Patchwork' and provides user with the choice to highlight information of one particular chromosome. The top plot shows clusters as regions of certain allelic constitution and copy number. The chosen chromosome is colored against a background of the complete genome in grey. A colored circle's gradient and size comply with the segment‘s position and size on the chromosome. The circles are semi-transparent so a darker hue, either colored or grey, indicates a greater amount of genomic content in that region. Regardless of the chosen chromosome, tags for copy number and allele content are also drawn on the plot. For example, 2m0 meas total CN is 2, minor CN is 0, homozygous and 3m1 means total CN is 3, minor CN is 1, heterozygous. The middle and the bottom panels respectively illustrate the normalized coverage and the total and minor copy number of the chosen chromosome. Between the two panels are the cytoband of the chromosome. To visualize data, upload a CSV file in the required format and use sidebar options to customize the display.

Single Sample Data

Check the official demo input here. User can directly use the output from the 'Patchwork' tool as our input file.

Display Interactions

There are three types of interactions: Tooltips and Download.

  • Tooltips
    When the mouse moves to a circle in the top plot, corresponding information like interval, size, allele imbalance, snv count and fullCN are shown on the tooltip.
  • Download
    One SVG file will be generated when the 'Download' button is clicked.

Sidebar Functions

The sidebar provides diverse options to manage files and select a chromosome.

  • Files
    • Manage Files: checklist of CSV files uploaded previously, delete or download the CSV files.
    • Upload: upload Single Sample CSV file. Note that the duplicated file name will be alerted and given a random postfix.
    • Choose: choose files uploaded previously. Note that this function is ONLY available to registered users (each account has certain storage).
    • File Sets: NOT available to this page.
  • Chromosome A selection box is provided to choose between all 24 chromosomes.

Manual version=1.1, written by Miss. LI Shiying and Dr. JIA Wenlong on 2020-02-06.

  1. MAYRHOFER, M., DILORENZO, S. and ISAKSSON, A. (2013). Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue. Genome Biology, 14(3):R24. (PMID: 23531354, See Figure 3)
  2. Chen, X. P., Long, X., Jia, W. L., Wu, H. J., Zhao, J., Liang, H. F., ... & Lin, L. (2019). Viral integration drives multifocal HCC during the occult HBV infection. Journal of Experimental & Clinical Cancer Research, 38(1), 261. (PMID: 31200735, See Figure S5)

Version

v1.0.3 (2020-02-06)

Developer

Mr. LI Hechen (GitHub)
Miss. LI Shiying (GitHub)

Designer

Dr. JIA Wenlong (Scholar, ORCID, GitHub)

Updates

v1.0.3

  • optimize tooltip content.
  • show tooltip on region segments.
  • show tooltip on cytoband.
  • show chr name beside chromosome.
  • optimize sidebar.

v1.0.2

  • fix circles lowering transparency after switching chromosome.

v1.0.1

  • add highlighting tracks on the middle and bottom panels as well as the corresponding circle in the top panel whenever mouse moves to one of them.
  • fix circles of the chosen chromosome being hindered by other circles.

v1.0.0

  • initial functions implemented.
Load