Best Graphics Gallery Or Blogs For Bioinformatics Use
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10.7 years ago
John ★ 1.5k

I am trying to compiling we resources for creating excellent visualization tools for bioinformatics use. The following are some of official graphics gallery I have found:-

R graphics gallery

Perl graphics gallery

Python-graph

sigma plot, not free

GNU plot

JMP Genomics (not free)

Specific plot library

Perl / circos plot

R / ggplot2
Blogs

R bloggers

R blogger, ggplot2 tag R blogger Lattice tag

R blogger visualization tag

Free GNU software

qgraph - plot interaction

Genetics and breeding tools

Are there other important library that are useful and specific to bioinformatics application? I think R should have better resources in this context. ..

graphs visualization genomics • 11k views
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Fairly related question asked recently here: http://biostar.stackexchange.com/questions/18378/packages-for-visualization-of-biological-data-in-r

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it is not related ..but not exactly...but discussion over there is relevant too..i am trying consolidate all visualization resources but not only R specific or program specific

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@malaching question is related but not exactly - as the question directed has attention on R packages not whole facinating world...also this question aims to collect gallery ...still discussion at your link is relevant too...

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I just posted a demo and some sample javascript code for displaying gene ontology as a force-directed graph using d3.js on my blog: http://blog.nextgenetics.net/?e=19

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10.7 years ago
Woa ★ 2.9k

One of my favourite graphics site:

http://cytoscape-publications.tumblr.com/

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6
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10.7 years ago
Raygozak ★ 1.4k

One visualization library related to chip-chip and chip-seq data, is the hilbertviz package.

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10.7 years ago
Neilfws 49k

See the R/Bioconductor View for visualization. I especially like GenomeGraphs.

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10.7 years ago
Flow ★ 1.5k

You should also consider matplotlib

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the library is nice ....

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4
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10.7 years ago

BALLView for a range of molecular modelling and visualization applications. One from their Gallery:

Pretty!

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That's pretty slick. Is this related to PyMOL (http://www.pymol.org/) somehow?

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The gallery has interesting stuff: http://www.ballview.org/Gallery

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There is python code, but I do not know of any connection to pymol. It is part Biochemical Algorithms [BALL] package.

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3
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10.7 years ago
Ram S ▴ 60

Here are some generic ones:

simple graph with r

quick-R

Specialized:

R / heat map plot

R / Manhattan plot

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3
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10.7 years ago

I've been using d3.js a lot. It's a great javascript library that you can use to create charts and diagrams in SVG format. Add Firebug or Chrome's console abilities, and you have a really nice method of creating your figures because you can step through your code and debug easily with the visual changes reflected instantly.

Here is a great beginner's tutorial for it assuming you have some knowledge of browser languages:

http://www.recursion.org/d3-for-mere-mortals/

Here is a really great video tutorial:

http://vimeo.com/35005701

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Lots of examples here that you can try out: https://github.com/mbostock/d3

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2
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10.7 years ago

Some python libraries:

Also, colorbrewer, pointed by russH, is a resource to choose good color palettes. It is useful when you have to draw a graph of some data and you want to know which colors to choose.

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10.7 years ago
Yannick Wurm ★ 2.4k

I think you wish (like me) that you had attended the Vizbi conference last week in Heidelberg: http://vizbi.org/

I think their unofficial aim is to increase the beauty of science :)

Luckily they have already uploaded some beautiful posters & I'm sure that some amazing talks will be uploaded too.

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whow !!!!! I wish I had attended this ...I see some videos as well ..nice

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10.7 years ago

There are two resources by Publishing Houses, that provide image search in articles. One from Springer - SpringerImages. Second is from Cell - CellImageLibrary. Of course they do have bioinformatics images.

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6.9 years ago
Collin ▴ 1000

If using python, consider the seaborn package (gallery here) which is built on top of matplotlib. It includes heatmaps, many statistical plots including linear models, mult-faceted/grid plotting, and color palettes (including colorbrewer). It leverages the pandas DataFrame object to make it easier for plotting then standard matplotlib. Personally, I like the figure aesthetics more than ggplot2.

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6.9 years ago

For color palette selection of charts, I use: IWantHue "Colors for data scientists"

They do k-means clustering of colors in a selected range to achieve maximum divergence between the individual colors. However, you can keep colors and re-cluster and similar thing to make it suit your needs.

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That's really good, I always struggle with this.

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10.7 years ago
SES 8.5k

If you want to create animations or explore high-dimensional data, GGobi is the tool to use. You can use it in R (package "rggobi") which is a great convenience. I would highly recommend a visit to r-forge, where you can search through lots of interesting projects with a wide range of bioinformatics applications.

For general plotting, you should consider GD, though you probably already have it if you generate graphics in BioPerl. Since you mentioned Perl, there is a great list of relevant modules on CPAN.

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10.7 years ago
Priyabrata ▴ 70

Though Its not related directly to Bioinformatics, still this site shows 50 great data vizualizations. We can implement these ideas on bioinformatics data with any of the tools listed above.

http://www.webdesignerdepot.com/2009/06/50-great-examples-of-data-visualization/

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6.9 years ago
yan1166 ▴ 10

I am developping a new R graph gallery. Have a look to

http://www.r-graph-gallery.com

All the best !

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10.7 years ago
Tyler Davis ▴ 20

You can use PathwayBuilder at http://www.proteinlounge.com or ePath3D which is available at the same site.

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6.9 years ago

Dear John,

I wrote this program to help me in my research: http://i-pv.org/

In a nutshell: it displays most protein features you can think of in an interactive interface that works for PC/mobile.

Here is an example: http://i-pv.org/FOXP2.html

Here you will find more examples and tutorial videos: http://i-pv.org/ipv_minimal.html

Regards

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6.9 years ago
rioualen ▴ 650

Rcharts looks pretty cool. It's not really specific to bioinformatics though.
http://rcharts.io/gallery/

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