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stianlagstad / chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
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What do the link widths represent in the overview plot? #41

Closed komalsrathi closed 6 years ago

komalsrathi commented 6 years ago

Hi Stian,

I was trying to create the overview plot but a little confused as to what the link widths mean here:

https://bioconductor.org/packages/release/bioc/vignettes/chimeraviz/inst/doc/chimeraviz-vignette.html#building-the-overview-plot

Initially I thought it represents how many times the event was observed. But the width between EDA-RFWD3 is greater than EEF1A1P5-PABPC1 even though EEF1A1P5-PABPC1 is seen 4 times and EDA-RFWD3 is seen only once. Can you please explain?

Thank you, Komal

stianlagstad commented 6 years ago

Hey @komalsrathi! The link width just signifies how many supporting reads (spanning + split) support that fusion event. But it's scaled compared to the other fusion events in the list. So that if you have this list of fusion events:

then the width of fusion3 would be the biggest. Does that make sense?

komalsrathi commented 6 years ago

Oh alright - I have been misunderstanding it as the number of times/samples it was seen in. Thanks for clarifying!