search

joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
577 stars 187 forks source link

What should a phyloseq logo be? #838

Open joey711 opened 6 years ago

joey711 commented 6 years ago

This is a copycat of the crowdsource polling for a DADA2 logo that has generated some awesome suggestions and prototypes.

Would love to see user suggestions / examples!

Cheers

Joey

joey711 commented 6 years ago

@spholmes I think you had at least one prototype... :)

spholmes commented 6 years ago

logo-phyloseqsmall logo-phyloseqhex2 logo-phyloseqt

spholmes commented 6 years ago

The Hex version for the sticker: (I was going to add an ordination in 3 d on top: too much going on)

[image: Inline image 1]

On Mon, Nov 6, 2017 at 7:17 PM, Susan Holmes sp.holmes@gmail.com wrote:

[image: Inline image 1]

On Mon, Nov 6, 2017 at 10:58 AM, Paul J. McMurdie < notifications@github.com> wrote:

@spholmes https://github.com/spholmes I think you had at least one prototype... :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/838#issuecomment-342249676, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcveve0ut5wPbJitSCpOXFwb8xV7iiks5sz1bfgaJpZM4QTtSy .

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

spholmes commented 6 years ago

[image: Inline image 1]

On Mon, Nov 6, 2017 at 7:17 PM, Susan Holmes sp.holmes@gmail.com wrote:

[image: Inline image 1]

On Mon, Nov 6, 2017 at 10:58 AM, Paul J. McMurdie < notifications@github.com> wrote:

@spholmes https://github.com/spholmes I think you had at least one prototype... :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/838#issuecomment-342249676, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcveve0ut5wPbJitSCpOXFwb8xV7iiks5sz1bfgaJpZM4QTtSy .

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

sfeds commented 6 years ago

Hi, I think the logo should show one of the strengths of phyloseq (in my humble opinion), which is the integration of all data into one easy-user-friendly package (i.e. otus, taxonomy and metadata) :)

DanielSprockett commented 6 years ago

What do you think about these rough concepts?

phyloseq_logo_1_DS.pdf

I don't think it does a great job communicating phyloseq's functionality(as @sfeds suggested), but I do think it is simple enough to scale well.

My other idea was to use the tips of either the "Y" or the "E" to evoke a sense of integrating multiple datasets. I couldn't think of a good way to illustrate taxonomy without using another tree or a (visually boring) table of taxonomic levels, but here is my attempt to play off the "phylo" and the "seq".

phyloseq_logo_2_DS.pdf

I could add circles to the tips of either tree to represent samples or metadata. In both cases, you'll probably want a better tree structure, but these were just images I had on hand.

Do you have any preferences in terms of capitalization? Or color pallets?

spholmes commented 6 years ago

This doesn't scale to the tiny format of the hex sticker (the problem I had too), please see some of the examples here for the size issue: https://github.com/Bioconductor/BiocStickers/tree/master/Biostrings https://github.com/Bioconductor/BiocStickers/tree/master/mzR

This is the same problem I had, also we sort have to keep the font compatible with all the other BioC stickers (see here:https://github.com/Bioconductor/BiocStickers).

On Sat, Dec 2, 2017 at 12:35 PM, Daniel Sprockett notifications@github.com wrote:

What do you think about these rough concepts?

phyloseq_logo_1_DS.pdf https://github.com/joey711/phyloseq/files/1524077/phyloseq_logo_1_DS.pdf

I don't think it does a great job communicating phyloseq's functionality(as @sfeds https://github.com/sfeds suggested), but I do think it is simple enough to scale well.

My other idea was to use the tips of either the "Y" or the "E" to evoke a sense of integrating multiple datasets. I couldn't think of a good way to illustrate taxonomy without using another tree or a (visually boring) table of taxonomic levels, but here is my attempt to play off the "phylo" and the "seq".

phyloseq_logo_2_DS.pdf https://github.com/joey711/phyloseq/files/1524127/phyloseq_logo_2_DS.pdf

I could add circles to the tips of either tree to represent samples or metadata. In both cases, you'll probably want a better tree structure, but these were just images I had on hand.

Do you have any preferences in terms of capitalization? Or color pallets?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/838#issuecomment-348718309, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcve3tuyd_oQjeY-O8s2RwVzLHPGwJks5s8bScgaJpZM4QTtSy .

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

joey711 commented 6 years ago

https://github.com/GuangchuangYu/hexSticker/blob/master/README.Rmd

grabear commented 6 years ago

I'm not sure who owns this image, but I really think it would work well here.

joey711 commented 4 years ago

I ran into someone, Anjile An at Columbia, at the RStudio::conf(2020) that drafted a really great version-1 sticker, IMO:

phyloseq

I'm thinking of sending to sticker mule and having some printed. Let me know if you want the .ai format for tweaking.

spholmes commented 4 years ago

Looks great, yes I will tweak maybe this weekend, maybe more Wes Anderson colors?

On Thu, Feb 13, 2020, 17:55 Paul J. McMurdie notifications@github.com wrote:

I ran into someone, Anjile An at Columbia, at the RStudio::conf(2020) that drafted a really great version-1 sticker, IMO:

[image: phyloseq] https://user-images.githubusercontent.com/841437/74494432-e0f72200-4e89-11ea-81e2-7787f809bc9f.png

I'm thinking of sending to sticker mule and having some printed. Let me know if you want the .ai format for tweaking.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/838?email_source=notifications&email_token=AAJFZPJCKSNNAGDB6B4OJ4TRCX22NA5CNFSM4ECO2SZKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELXJCDY#issuecomment-586060047, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJFZPLBCVYR4CNGFTMD3ETRCX22NANCNFSM4ECO2SZA .

joey711 commented 4 years ago

@spholmes I thought you might like the Stanford Cardinal red O:-) It took some arm-twisting, as the creator is a Cal alum! I do also quite like the earlier one you posted with the cube and the wiggly tree inside. We might be able to get her to take a crack at that one to simplify enough to work in a tiny hex sticker. I'll ask her on twiiter: @anjile_an

joey711 commented 4 years ago

Looks great, yes I will tweak maybe this weekend, maybe more Wes Anderson colors? … On Thu, Feb 13, 2020, 17:55 Paul J. McMurdie @.***> wrote: I ran into someone, Anjile An at Columbia, at the RStudio::conf(2020) that drafted a really great version-1 sticker, IMO: [image: phyloseq] https://user-images.githubusercontent.com/841437/74494432-e0f72200-4e89-11ea-81e2-7787f809bc9f.png I'm thinking of sending to sticker mule and having some printed. Let me know if you want the .ai format for tweaking. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#838?email_source=notifications&email_token=AAJFZPJCKSNNAGDB6B4OJ4TRCX22NA5CNFSM4ECO2SZKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELXJCDY#issuecomment-586060047>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJFZPLBCVYR4CNGFTMD3ETRCX22NANCNFSM4ECO2SZA .

I am fine with other colors, though. I like the Wes Anderson palette.