Join GitHub today
GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.
Sign upVisualization Enhancement #3
Comments
This comment has been minimized.
This comment has been minimized.
The plot might become pretty crowded if multiple peaks are close to each other though. Anyway:
|
This comment has been minimized.
This comment has been minimized.
schymane
commented
Oct 5, 2019
If you select the most intense peak within a certain window (e.g. 10 mz, or scale the window with the max(mz) so it's a larger window for higher mz spectra) for annotation, you will be able to avoid most overlap automatically, but still be informative (at least those values are what worked for us in R). Depends how you wish to orient the text. I piggybacked off the satellite peak filtering in RMassBank: |
This comment has been minimized.
This comment has been minimized.
I could easily implement Emma's suggestion within the app... |
This comment has been minimized.
This comment has been minimized.
Done - it's a bit messy, but we can tidy up.
|
This comment has been minimized.
This comment has been minimized.
schymane
commented
Oct 6, 2019
Can we have 4 dp please? Or an option to add more than 2? It's essential for interpretation. |
This comment has been minimized.
This comment has been minimized.
Done...will be online next time Ming updates |
This comment has been minimized.
This comment has been minimized.
Awesome! Just saw the thread. I made a few changes to display both the unlabled and labeled SVG in the default plot: https://metabolomics-usi.ucsd.edu/spectrum/?usi=mzspec:GNPSLIBRARY:CCMSLIB00000840338 Deployed live, cutting release. Thanks @schymane @sdrogers @bittremieux @alan-jarmusch. Ming |
This comment has been minimized.
This comment has been minimized.
schymane
commented
Oct 10, 2019
Looking great! Tiny suggestion, if you tilt the masses on an angle (eg 25-30 degrees?) you'll avoid it crossing the line and it makes it easier for people to read ... |
This comment has been minimized.
This comment has been minimized.
Awesome, will make issue about suggestion! Going to also add issue integrating massbank. If you have a web api should be super easy to integrate. |
This comment has been minimized.
This comment has been minimized.
these are looking really great! [image: image.png]
…On Thu, Oct 10, 2019 at 12:07 PM Ming Wang ***@***.***> wrote:
Awesome, will make issue about suggestion!
Going to also add issue integrating massbank. If you have a web api should
be super easy to integrate.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#3?email_source=notifications&email_token=AJ3E7DSVNEM3Z6G2WU6ZVRDQN54PPA5CNFSM4I5UFCF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEA5O4UA#issuecomment-540733008>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AJ3E7DS2TYR4DVGMPAYR7J3QN54PPANCNFSM4I5UFCFQ>
.
--
Alan K. Jarmusch, PhD
alanjarmusch@gmail.com
|
This comment has been minimized.
This comment has been minimized.
@bittremieux if you are responsible for the italics on m/z... then kudos |
This comment has been minimized.
This comment has been minimized.
I'm actually not a big fan of the rotated peak labels because that way they can overlap with neighboring peaks. |
This comment has been minimized.
This comment has been minimized.
schymane
commented
Oct 11, 2019
yes I see what you mean, my x axis is usually much more stretched wrt y so it works better as the peaks are more spread out. Maybe add this as an option that people can adjust? Vertical is very difficult to read, and some like horizontal even if this overlaps even more ... |
alan-jarmusch commentedOct 4, 2019
provide m/z labels for peaks >5% intensity