Feature properties > color assignment

[gmcarthuriv]

Request: The ability to assign colors to GenBank features

[tnrich]

@gmcarthuriv do you have a preference for what color palette to make accessible? Should any color be available?

cc @mfero @njhillson

Also here is a list of color pickers that we could choose from if we want to: https://casesandberg.github.io/react-color/

Let me know if anyone has a preference on palette (or lack thereof) and color picker type

[njhillson]

Hi @tnrich there is a standard/branded palette for JBEI. I imagine each company may want their own custom palette. However, I imagine for any given instance (company) having a consistent palette/coloring scheme for a given feature type would be a good idea. Multiple allowed colors for the same feature type could be confusing...

On Fri, Jan 19, 2018 at 2:00 PM, Thomas Rich notifications@github.com wrote:

@gmcarthuriv https://github.com/gmcarthuriv do you have a preference for what color palette to make accessible? Should any color be available?

cc @mfero https://github.com/mfero @njhillson https://github.com/njhillson

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[tnrich]

@njhillson I definitely agree that having a standard color for each feature type is desirable but it sounds to me like @gmcarthuriv wants to be able to sometimes change a given feature's color to a color different than it's default type-based color. Correct me if I'm wrong @gmcarthuriv

[njhillson]

Ok, would be good for @gmcarthuriv https://github.com/gmcarthuriv to specify if this is, for example, just a request for an Arzeda-standard color palette that is distinct from TeselaGen default (but that normal users can't change), or if he wants any one (pending user role I suppose) to be able to chose a custom color for any particular feature within the Arzeda instance.

On Fri, Jan 19, 2018 at 2:18 PM, Thomas Rich notifications@github.com wrote:

@njhillson https://github.com/njhillson I definitely agree that having a standard color for each feature type is desirable but it sounds to me like @gmcarthuriv https://github.com/gmcarthuriv wants to be able to sometimes change a given feature's color to a color different than it's default type-based color. Correct me if I'm wrong @gmcarthuriv https://github.com/gmcarthuriv

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[gmcarthuriv]

@tnrich, @njhillson,

Apologies for the delay. My thoughts:

• "Multiple colors for the same feature type could be confusing..." For common features such as CDSs, yes. However, it would be really handy to be able to color different misc_feature labels with different colors. That is, there are often a myriad of misc_feature labels (as shown in the example below). Color could be a nice parameter to differentiate various sub-types (e.g., insulators).
• Currently there is a lot of color sharing between feature types. For example (again, shown below), misc_feature labels and RBS labels use the same color (grey). In fact, most features use grey (if I remember correctly), which is not very useful.
• It would be really cool to able to assign any color to any feature type using hex codes or by picking from a more-constrained color "theme" specific to Arzeda, but not necessary. That is, being able to pick from a standard set of colors is sufficient (e.g., http://clrs.cc/).

Given the above comments, my suggestion is to allow the user to 1) assign colors (from a standard set) to feature types and 2) allow the creation of multiple misc_feature types to align better with current synthetic biology practices. For example, within the app a user could define a GenBank feature type "insulator" (misc_feature_insulator) to correspond with the SBOL genetic part concept. It would be displayed as a GenBank feature within OpenVE. Upon export, these custom features would be collapsed into a single GenBank feature type "misc_feature" so that it would render correctly in ApE, etc.

[tnrich]

Hey @gmcarthuriv I think what you're saying makes sense.

You're also totally right about many of the features defaulting to grey. I will set better defaults for those.

Maybe as a first step I'll make a color picker that lets you choose any color for any feature, and then as a second step allow you to change the default color for given feature types.

@njhillson the color picker will not be enabled by default, only if a config option is passed that turns it on.

[njhillson]

misc_feature subtypes (extending GenBank) sounds fine to me. Upon export reverting to misc_feature seems sensible.

better standard colors would be good (enabling admin to set these).

I would suggest keeping this an admin feature, to set the color for each feature type for the whole instance. However, if @gmcarthuriv / Arzeda wants each user to be able to independently to do this, one question would be do I look at someone else's plasmid map with my preferred pallet, or the one they used? Just a thought experiment...

On Tue, Jan 23, 2018 at 10:33 AM, Thomas Rich notifications@github.com wrote:

Hey @gmcarthuriv https://github.com/gmcarthuriv I think what you're saying makes sense.

You're also totally right about many of the features defaulting to grey. I will set better defaults for those.

Maybe as a first step I'll make a color picker that lets you choose any color for any feature, and then as a second step allow you to change the default color for given feature types.

@njhillson https://github.com/njhillson the color picker will not be enabled by default, only if a config option is passed that turns it on.

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[gmcarthuriv]

I agree; it would be best to implement this across the entire company (i.e., an admin determines the color scheme and is locked to all other users).

[gmcarthuriv]

@tnrich, @tiffanydai, @craftjk, @siobhandavis,

Is this ticket still active? Please let me know if there's anything I can do to help.