Please try the demo file in the sidebar (Demo File Sets).

Introduction

The 'Context' visualization, otherwise known as the 'Lego plot' of mutational frequencies, describes the distribution of mutations across batch samples on a given region. Base substitutions are divided into six types to represent the six possible base changes (each type represented by a different color as shown in the “Mutation Type” legend). Substitutions in each type are further subdivided by the 16 possible flanking nucleotides surrounding the mutated base as listed in the “Trinucleotide Context” table. The pie chart illustrates the percentage of all mutations types in said batch samples.

Input Files

Check the official demo input here.

SNV File

Note that backend annotation task will be activated once the SNV file is uploaded. User could check the job status in task monitor at the bottom of this page.
This input file could be standard MAF file (see format) or VCF file.
Or, a simple TSV file in the format specified below.

#contig	position	ref_allele	alt_allele	tumor_f
chr1	101686	A	G	0.113636

• the first line should be the header as specified above.
• # prefix is mandatory to indicate the header line.
• contig and position respectively stand for the chromosome and position of the mutation.
• ref_allele and alt_allele respectively stand for the base before and after the mutation.
• users could filter mutations with tumor_f value by custom condition in the sidebar.
• NOTE that the tumor_f is optional, i.e., this column could be omitted.

Custom BED File (optional)

A custom bed file allows users to replace the default region used in our website, which is the whole genome sequence. We will filter out mutations that are not in the custom region during the calculation. Note that the uploaded bed file is only applied when you choose the custom bed option in the Settings section of the sidebar.

The uploaded BED file must match the required format as specified below (please keep the header).

#chr	startPos	endPos
chr1	11174854	11175054

Display Interactions

There are three types of interactions: Tooltips, Transparent Bins and Download.

• Tooltips
  A tooltip shows necessary information of the object the mouse points to.
  • bin: A tooltip is drawn when the mouse lands on the bottom of a bin. The displayed information includes the mutation type and the trinucleotide context represented by this bin as well as the exact height of the bin.
  • pie: A tooltip is drawn when the mouse moves to a certain arc of the pie chart and shows the exact percentage of the corresponding mutation type among all mutations.
• Transparent Bins
  When the mouse lands on the bottom of a bin, the bottom will be highlighted and all bins before it will become transparent to avoid hindered view.
• Download
  One SVG file will be generated when the 'Download' button is clicked. Only the default Dark Theme is available at this point.

Sidebar Functions

The sidebar provides diverse options to fine-tune the display, namely managing files, adding labels on bins, choosing base regions and setting the measurements of mutations.

• Files
  • Manage Files: checklist of TSV files uploaded previously, delete or download said BGZ files.
  • Upload: upload batch sample BGZ file and the optional bed TSV 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: save a batch sample file and a bed file together as a file set. Users can also choose to apply one file set from all saved ones.
• Labels
  • Label Buttons: choose a symbol (except for the first and the last button) to enter labeling mode. In this mode, when you click a bar, the corresponding symbol will be added to the bar as an annotation.
  • Off Button: click this button to exit from labeling mode. Re-click to re-enter labeling mode with the last-used symbol.
  • Remove Button: click to enter removing mode. In this mode, when you click a bar with a symbol, the corresponding symbol will be removed.
• Setting
  
  • Interval: choose between the default region and the custom region. If no bed file is provided, the only option is the default whole genome region.
  • Y axis: provide three measurements of the mutation count, namely the numeric sum of the mutation, mutations per Mb and the percentage among all mutations.
  • Filter by tumor_f: choose the compare method and the threshold for filtering mutations.

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