Anyone knows how to create a figure like this?
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3.0 years ago
Alexie Li ▴ 20

Horizontal axis indicate features on chromosomes. Y axis displays multiple chromosomes.

Thank you!

Best wishes,

Alexie Li

genome visualizaion tool • 1.6k views
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This is more of a comment, than an answer, but jrj.healey's answer is perhaps a better match than a typical "joy plot", as it renders the z-axis at an angle. However, another option that may be less confusing is a 2D heatmap. It doesn't rely on your audience guessing at the y-axis or "height" of the datapoint, which already has an ambiguous x-axis position, by shifting the z-axis off-center.

A 2D heatmap gives you a strict grid of chromosome rows, genomic position columns, and cells are colored from low to high saturation based on some normalized numerical scale (your example plot's antisense/sense ratio). A 2D heatmap may be less visually exciting than a modified joy-plot, but it will also be less ambiguous in terms of interpretation.

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If this is from the publication, please provide the link to the paper, so we can see the context, then maybe we could suggest a better visualisation. At the moment, it looks like there is no need to make the y-axis tilted.

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Check this post from a few hours ago, providing a lot of links to previous posts on this.

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It's not a 2D plot, it's 3D. Maybe try plots allowing 3 axes including categorical data?

EDIT: nevermind, I see that a link was added above by ATpoint. We really need a way to promote in-line replies as the answer.

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@ATPoint is only referring to a thread from earlier today which has several relevant links already posted.

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If such replies answer the question, they can always be moved to an answer by a moderator.

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Of course, but it seems this seldom happens. I'm guessing it's b/c doing so requires the submitter to request this of a moderator?

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Once you have >200 rep (I think), you can moderate your own posts, including moving comments to answers etc.

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Chris Fields : Mods keep a close watch but would be happy to know of any candidates that we may miss. You are welcome to join the biostar slack channel biostar.slack.com) and post those links in #general channel.

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3.0 years ago
igor 12k

It wouldn't be the same, but you can make a similar plot with ggridges R package: https://cran.r-project.org/web/packages/ggridges/vignettes/introduction.html

One example:

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3.0 years ago
Joe 19k

Looks similar to a waterfall plot to me, but with more discrete data.

You can make nice 3d plots like this with plot_ly in R.

Its not totally clear to me what the Z axis is counts of, but it should be easy enough to plot.

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