Coder Social home page Coder Social logo

Comments (1)

slinnarsson avatar slinnarsson commented on May 28, 2024

As I explain in #2629 I think the proper way to plot single-cell data is to first plot the zeros in light grey, then plot non-zeros using a colormap, on top. As long as point overlap is kept to a minimum (often also an issue in cellxgene), this way of plotting accurately reveals both low and no expression.

For example, consider the difference for AQP4 expression in this example of glioblasts when using grey for zeros (left) or just using the colormap (right):

image

When just using a colormap gradient, the true structure of gene expression disappears. Plotting low-to-high will not make any difference to the plot.

from cellxgene.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.