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sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
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Trees #24

Closed nirshahaf closed 3 years ago

nirshahaf commented 3 years ago

Apologies for opening 2021 with so many Issues...

A previous Sirius version had the option (now apparently cancelled) to generate fragmentation tree in the .dot format, which could then be rather easily converted to figures via a third party app. However current version generates only .json files. Can you perhaps add to the documentation an outline of a procedure from .json tree files to a graphical tree representation (as was previously outlines for the .dot files)?

mfleisch commented 3 years ago

The graphical user interface of SIRIUS offers tree export as svg,pdf,dot and json format. You can open an already computed project and export the trees you want as vector graphics or dot.
treeExport

nirshahaf commented 3 years ago

The GUI is super nice, but could you perhaps list the internal functions (or library dependencies) which produce the tree? I would like to generate a batch procedure for this task, if possible.

mfleisch commented 3 years ago

We add the tree export as json and dot as standalone tool to the CLI. A new build including this features will be available in the next days.

nirshahaf commented 3 years ago

Hi Markus,

Fair enough, but in this case I think it's also necessary to merge back the missing documentation explaining how to convert using 'GraphViz'. In version manual 4.0.1 it's found under the headline 'Visualizing fragmentation trees'.

Thanks!

mfleisch commented 3 years ago

Dot file export now available in SIRIUS 4.6.0 via the ftree-export tool. The documentation has also been updated regarding dot export and conversion.