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Topic: networks (Read 548 times) previous topic - next topic

networks

Hi Hiroshi,

I am currently experiencing a crash of MS-DIAL when trying to export the molecular network file (GC-MS data).   Could you look into that?

Interestingly, the network is processed and the visualization works fine using the menu --> Data Visualization, even in Chrome seems to work.

About the network visualization in the browser, it would be nice if possible, to add the options to:
- change the network layout (at the moment it is very dense)
- color by sample category

This I would do in Cytoscape, but at the moment I cannot export the file :)

Best,

Stefano

Re: networks

Reply #1
Hi Stefano,

thanks, I did not realize the issue, and I fixed it today.
I will upload the new version of MS-DIAL as soon as possible, and from next version, you can export the node and edge files to be used in cytoscape.

Thanks,

Hiroshi

Re: networks

Reply #2
Hi Hiroshi,

that´s great!

If it is not a big issue, would it be possible for you to also already in the next version, that when using the function to export the spectra (in .msp) from the Alignment, we also get reported as the "Name", the aligned variables (e.g. in order, ID 1, ID 2..) corresponding to the order in the matrix tables? At the moment we only have either "Unknown" or the putative metabolite.
That would be super useful for when importing the msp into NIST!

Thanks

Stefano

Re: networks

Reply #3
Before the new version is out, if someone is using python, I fix it like this:
(it will create a new file with the "Align ID)

data = open('spectra_test_MS-DIAL.msp', 'r')
data_new = open('spectra_test_MS-DIAL_new.msp', 'w')

counter=0
for line in data:
    stuffinline = line.split()
   
    if stuffinline != []:
        first_element = stuffinline[0]
        second_element = stuffinline[1]
        if first_element == "NAME:":
            counter+=1
            second_element_new = "Aligned ID #" + str(counter)+ " - " + second_element + "\n"
            line = first_element + second_element_new
   
    data_new.write(line)