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krassowski / multi-omics-state-of-the-field

Analyses for "State of the field in multi-omics research: from computational needs to data mining and sharing"
https://doi.org/10.3389/fgene.2020.610798
MIT License
24 stars 13 forks source link

Add analysis flowchart #24

Closed krassowski closed 4 years ago

krassowski commented 4 years ago

Closes #15. Initially i tried mermaid-based flow graph:

Screenshot from 2020-08-05 02-53-10

but I could not get handle of its layout (probably should have stuck to dot or html), so I ended up re-doing it manually:

Screenshot from 2020-08-05 02-59-21

My idea was to put it next to the other figure that we have to save space... but I can also re-layout this...

Please let me know your thoughts.

krassowski commented 4 years ago

The icons could be added to the manual version too, but those are CC-BY 4.0 and would need attribution on the figure (just 3-4 words in the corner would do). Anyways, just wanted to show this as an option. Maybe adding the attribution text added is not a high price for improving the ease of interpretation of the chart.

vd4mmind commented 4 years ago

So I kinda a like the first one as it has some logos or widgets to distinguish things. However I would have thought of it a bit narrowed so as to not hand the bends of arrows like that. If go I want to keep the second one I would actually redo it like the first only to modify the connectors properly to keep within a space limit. The second one is clear to me but I feel others might not get the connections and branchings. They might think it’s seqeuntial top down which isn’t. Is it possible to modify something manually like the first one. Also add the final numbers there in the end panels.

krassowski commented 4 years ago

What about?

Screenshot from 2020-08-05 04-14-42

I think that the linear one is better (no wasted space), and I do not think that following arrows is that hard... they do not even cross..

vd4mmind commented 4 years ago

Hi Mike,

This one looks better to me. Much clearer than both. I approve this. Now you can just freeze them and start preparing the e-mail for Biswa.

Best,

Vivek

biswapriyamisra commented 4 years ago

Looks good either this one or linear one, on line journal so space or white would not matter much. Certainly can be a Figure 5 for peer-review and then go from there. I have minor edits on the figure as you can see below (and will wait for its captions/ explainer?)

[image: image.png]

On Wed, Aug 5, 2020 at 8:46 AM Michał Krassowski notifications@github.com wrote:

What about?

[image: Screenshot from 2020-08-05 04-14-42] https://user-images.githubusercontent.com/5832902/89367945-36421c80-d6d2-11ea-8bbb-60b145927396.png

I think that the linear one is better (no wasted space), and I do not think that following arrows is that hard... they do not even cross..

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vd4mmind commented 4 years ago

Biswa, this should be figure 4 as this is the systematic flow diagram that tells us how Mike generated multi panel figure. Or do you want this to be the last figure? As I was thinking that readers gets to understand the self explanatory flow diagram to generate the data that finally led to the multi panel plots and our inferences.

krassowski commented 4 years ago

That's why I wanted to merge it with the multi-panel figure as a tall column to the left ;) But either is fine with me!

@biswapriyamisra I cannot see your image - unfortunately the attachments do not work great if you repy from e-mail, you need to login to GitHub and add it here. I need to go get some sleep it's nearly 5am here so will reply later..

krassowski commented 4 years ago

Also, If you are happy with a small attribution text in the corner ("Icons CC-BY 4.0 Font Awesome"), then I am happy to add the icons!

vd4mmind commented 4 years ago

Hi Mike,

Just emailed you want Biswa tried to ask. Check your gmail once. I am unsure how to put it here as I am writing from my phone.

vd4mmind commented 4 years ago

Ah, that’s pretty late. Take rest now. I will touch base with Biswa

biswapriyamisra commented 4 years ago

That's alright for now!

Thanks, Biswa

On Wed, Aug 5, 2020 at 9:28 AM ivivek87 notifications@github.com wrote:

Ah, that’s pretty late. Take rest now. I will touch base with Biswa

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krassowski commented 4 years ago

Addressing Biswa's comments:

krassowski commented 4 years ago

Screenshot from 2020-08-05 14-05-12

krassowski commented 4 years ago

Just tell me if I you are ok with including the icons and attribution, please and then I will sent an updated vector file and solve this!

biswapriyamisra commented 4 years ago

Sure do it, and send the final figure back to us! : )

On Wed, Aug 5, 2020 at 6:36 PM Michał Krassowski notifications@github.com wrote:

Just tell me if I you are ok with including the icons and attribution, please and then I will sent an updated vector file and solve this!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/krassowski/multi-omics-state-of-the-field/pull/24#issuecomment-669181977, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGUCRIBUG4DR4ZNWUJGYMIDR7FKNRANCNFSM4PU7LU2Q .

krassowski commented 4 years ago

Raster here:

Screenshot from 2020-08-05 15-16-34

I will e-mail you a PDF soon.

vd4mmind commented 4 years ago

@krassowski fantastic. Looks great. :)