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Home Page: https://explosig.lrgr.io
License: MIT License
ExploSig: web-based interactive visualization of mutation signatures and somatic mutation data
Home Page: https://explosig.lrgr.io
License: MIT License
Buses are nicer than watchers ($emit, $on)
see https://alligator.io/vuejs/global-event-bus/
https://www.nature.com/articles/nature12477/figures/1
mutations per megabase
deconstruct by mutation category or mutation base substitution type
prevent dispatching,etc when using local files
Rearrangements are hypothesized to associate with kataegis. It would be interesting to add rearrangement "breakpoints" to the rainfall plot.
To get the breakpoints, you would structural_somatic_mutation files, e.g. for BRCA-EU at this link:
https://dcc.icgc.org/releases/release_26/Projects/BRCA-EU
No requests should specify chromosomes, just fetch data for all, then show/hide on front end
will require adding svg xmlns attributes everywhere
and figuring out weird axis tick text positioning
Same process as minimum bar width for exposures plot
Allow user to drag along a bar above/below genome-wide plots to show a different chromosome
Possibly just never limit to single chromosome, always load data for all (kind of already done for kataegis plot)
If so, create plots for all chromosomes, with only a single one visible initially (think of as window)
Plots that use aggregated data
non-COSMIC signatures:
Give each signature a name, a source - publication, and an index
Sort by publication, then index
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ possibly use refFlat.txt.gz file
exons, transcripts, promoter regions?
possibly see http://epiviz.cbcb.umd.edu/4/
Choose a different set of signatures, plot differences in exposures
Not separate for each plot
Look into using VAF to visualize clonality
Will probably need to retain duplicate donor reads/samples to do so
Think about this more
https://www.biorxiv.org/content/early/2018/02/05/260471
Local file reading works in Firefox but not chrome
https://bl.ocks.org/mbostock/5872848
https://github.com/d3/d3-dispatch
See how MAGI implements this http://magi.brown.edu/
limit redundant code
Relates to #34
not urgent, but would be nice to work in at least:
Upon addition of new plot, show small animation to indicate where dragging functionality is enabled
see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5477513/ supplement 1 pg 4
number of mutations per sample, by signature exposure, comparing smokers/non-smokers and <60/>=60 yr olds
save whether single donor or all donor mode
very minor
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