Skip to content
Please note that GitHub no longer supports your web browser.

We recommend upgrading to the latest Google Chrome or Firefox.

Learn more

/MetabolomicsSpectrumResolver

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Improving the fragment m/z value display #4

Open
lfnothias opened this issue Oct 10, 2019 · 4 comments

Comments

@lfnothias
Copy link

commented Oct 10, 2019

  • First view: Enable the toolbox tip by default
  • SVG: Have a user defined value for the m/z intensity threshold.
sdrogers added a commit that referenced this issue Oct 10, 2019
@sdrogers
Plot labeling and refactoring #4
25318f5 
- Added a thresh parameter so the user can define the threshold (relative) for plotting. Default is everything above 0.1 is plotted
- renamed labels_emma method to just labels and deleted old one
- tidied up plot parameter passing into a single dictionary
- Still need to change default tooltip for the interactive plot...
@schymane

This comment has been minimized.

Sign in to view
Copy link

commented Oct 10, 2019

May also need to auto detect appropriate decimal places from input data (if only 1 dp in input, we should not display 4)
@schymane

This comment has been minimized.

Sign in to view
Copy link

commented Oct 10, 2019

Also (I'm mobile viewing atm) may need more buffer on y axis so masses don't cross plot border
@bittremieux

This comment has been minimized.

Sign in to view
Copy link
Collaborator

commented Oct 10, 2019

Y-axis scaling is a bit annoying. I've looked into ways to do it dynamically within spectrum_utils, but that's pretty much impossible because you can't know where the text annotations will end up before painting the figure, and after painting you can't change anything anymore.

In spectrum_utils I use 1.05 as y_max when peaks aren't annotated and 1.15 when they are. To properly fit a 7-digit number (4 decimals) the 1.15 might have to be increased a bit.
@schymane

This comment has been minimized.

Sign in to view
Copy link

commented Oct 11, 2019

I tend to hard code as well, up to 1.5 for mass annotations and 2.5 if you want formula and structure annotations ...
The basis of the spectra in here were autogenerated, if you want to get an idea. 2.5 may be overkill but does leave lots of space for annotations ...
https://link.springer.com/article/10.1007%2Fs00216-019-01885-0
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
3 participants
@lfnothias @schymane @bittremieux
You can’t perform that action at this time.