Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Customize structure plot #7

Open
AMA-cs opened this issue Nov 21, 2024 · 0 comments
Open

Customize structure plot #7

AMA-cs opened this issue Nov 21, 2024 · 0 comments

Comments

@AMA-cs
Copy link

AMA-cs commented Nov 21, 2024

Hello @fjossinet ,

I've recently started exploring RNArtistCore and I really appreciate the flexibility and customization options it offers. However, there are a few features or customizations I’m particularly interested in, and I couldn’t find clear information on them. I wanted to check if they are already available or if I’m possibly missing something.

  1. Gradient Coloring for Pairing Probability
    I noticed that RNArtistCore allows for gradient coloring based on reactivity or pairing probability using the "data" and "color" element (with value, to, etc.). However, I was wondering if there's a smoother variation for coloring when using pairing probability values as data. Specifically, when trying to replicate the coloring used in RNAfold, I find I have to assign a color to each range manually, but this approach doesn’t provide a smooth transition. Is there an alternative way to achieve a smoother gradient besides the method I’m using with more than two colors?

  2. Hiding Specific Parts of the Structure
    I tried using the "hide" element, but it doesn’t completely hide the location I specified. Is there a way to specify certain parts of the structure to draw while skipping others? I'd like to hide specific regions more effectively.

  3. Labeling Nucleotides with Custom Text
    Is there a way to label specific nucleotides with custom text (rather than the default nucleotide numbering)? It would be helpful to display custom names for selected nucleotides, similar to how the nucleotide numbering is shown.
    Thank you for your help, and I look forward to your response!

4- Pairing Line
From the plot below, you can see the black line that crosses the loop (with two circles, at 536 & 527 and also at 519 and 520). I'm not sure I know what the black circles represent. Could you clarify that for me please? and is there a way to make the line at 536 shorter like any other pair (second image)
image
image

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant