hydrophobicity color_theme

[TangYiChing]

Hi,

Can you clarify how hydrophobicity is defined and the color coding for hydrophobic, hydrophilic, and neutral, respectively

[jbkinney]

These are just meant to be the standard physical property classifications of amino acids; we’re not working off of a specific rigorous definition. Do you see an error?

Cheers, -Justin

Justin B. Kinney, PhD
Associate Professor
Simons Center for Quantitative Biology
Cold Spring Harbor Laboratory
***@***.***
631-897-5731

On Aug 12, 2024, at 12:43 PM, Yi-Ching Tang @.***> wrote:

External email.

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Hi,

Can you clarify how hydrophobicity is defined and the color coding for hydrophobic, hydrophilic, and neutral, respectively

— Reply to this email directly, view it on GitHubhttps://github.com/jbkinney/logomaker/issues/39, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABXOC3GF6KVCTY2YLJTL633ZRDQ4BAVCNFSM6AAAAABMMRKXM6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ3DCNBWGI3DCOA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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[TangYiChing]

Thank you for the clarification. I don't see any errors, but I want to ensure I fully understand every detail on the graph before presenting it. The diverse color theme is effective when it conveys the intended message clearly.

As hydrophobicity can be interpreted through various measures, such as the Kyte-Doolittle (KD) scale, I wanted to ensure that my interpretation aligns with the intended message of the graph. Having color codes for these different properties could enhance the clarity and impact of the visualization.

[jbkinney]

Your question is a good one. I would say don’t trust our classifications of the amino acids. We just took this classification (and color scheme) from some other (not properly documented) source. If you want to make a rigorous map yourself, I suggest using a custom coloring scheme that you define.

Cheers, -Justin

Justin B. Kinney, PhD
Associate Professor
Simons Center for Quantitative Biology
Cold Spring Harbor Laboratory
***@***.***
631-897-5731

On Aug 12, 2024, at 10:38 PM, Yi-Ching Tang @.***> wrote:

External email.

---

Thank you for the clarification. I don't see any errors, but I want to ensure I fully understand every detail on the graph before presenting it. The diverse color theme is effective when it conveys the intended message clearly.

As hydrophobicity can be interpreted through various measures, such as the Kyte-Doolittle (KD) scale, I wanted to ensure that my interpretation aligns with the intended message of the graph. Having color codes for these different properties could enhance the clarity and impact of the visualization.

— Reply to this email directly, view it on GitHubhttps://github.com/jbkinney/logomaker/issues/39#issuecomment-2285234097, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABXOC3BFGO6N5WSVNGRRVH3ZRFWSBAVCNFSM6AAAAABMMRKXM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOBVGIZTIMBZG4. You are receiving this because you commented.Message ID: @.***>

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[TangYiChing]

That's cool - customized coloring scheme. I will look into that. Thank you!