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ElucidataInc / ElMaven

LC-MS data processing tool for large-scale metabolomics experiments.
https://resources.elucidata.io/elmaven/
GNU General Public License v2.0
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Change format of clipboard data for peak group - add formula, separate label #680

Open lparsons opened 6 years ago

lparsons commented 6 years ago

Currently, when a user double clicks a peak or selects the "Copy isotope information to clipboard" option from the context menu, they get a table with the columns for the Compound | Isotope Label and one column for each sample with the integrated intensities. This is not ideal for isotope correction, and in fact can't be used by Polly. We propose to change the format to:

  1. Formula
  2. Compound Name
  3. Label
  4. Sample 1
  5. Sample 2
  6. ...

In addition, the sort order of the clipboard data doesn't sort numerically on label counts, which isn't convenient (C13-label-1, 10, 11, ..., 2, 20, etc.). It should match the default sort order of the bookmarks table.

Inspiration for format: http://docs.elucidata.io/Polly-Iso-Correct/index.html

sp-eldata commented 6 years ago

This kind of column name challenge seems to happen frequently. Is that so? If yes, should we have a consistent way to handle it?

Also, export format changes should be discussed.

On Wed, Apr 18, 2018 at 10:06 PM, Lance Parsons notifications@github.com wrote:

Currently, when a user double clicks a peak or selects the "Copy isotope information to clipboard" option from the context menu, they get a table with the columns for the Compound | Isotope Label and one column for each sample with the integrated intensities. This is not ideal for isotope correction, and in fact can't be used by Polly. We propose to change the format to:

  1. Formula
  2. Compound Name
  3. Label
  4. Sample 1
  5. Sample 2
  6. ...

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ElucidataInc/ElMaven/issues/680, or mute the thread https://github.com/notifications/unsubscribe-auth/AVnbMfvgEjxFrKBsbt754irMDKIC6bHJks5tp2tzgaJpZM4TaZS1 .

chubukov commented 6 years ago

We don't rely on the clipboard format for any processes, so I don't have any opinions here.

lparsons commented 6 years ago

Thanks, I hope this can be fast tracked, as many here do use the copy-paste due to stability issues (esp in classic Maven), the complex output format of the csv export, and the difficulties of working with the bookmarks table (clunky compared to Excel). The current copy/paste doesn't even include the compound at all.