Question: Best Graphics Gallery Or Blogs For Bioinformatics Use
34
gravatar for John
6.8 years ago by
John1.4k
John1.4k wrote:

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. ..

visualization genomics graphs • 7.3k views
ADD COMMENTlink modified 2.9 years ago by Manuel Landesfeind1.1k • written 6.8 years ago by John1.4k

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

ADD REPLYlink written 6.8 years ago by Malachi Griffith17k

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

ADD REPLYlink written 6.8 years ago by John1.4k

http://colorbrewer2.org/

ADD REPLYlink written 6.8 years ago by Russh1.2k

@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...

ADD REPLYlink written 6.8 years ago by John1.4k

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

ADD REPLYlink written 6.7 years ago by Damian Kao15k
7
gravatar for Woa
6.8 years ago by
Woa2.7k
United States
Woa2.7k wrote:

One of my favourite graphics site:

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

ADD COMMENTlink written 6.8 years ago by Woa2.7k
6
gravatar for Raygozak
6.8 years ago by
Raygozak1.2k
State College, PA, Penn State
Raygozak1.2k wrote:

One visualization library related to chip-chip and chip-seq data, is the hilbertviz package, http://www.ebi.ac.uk/huber-srv/hilbert/

ADD COMMENTlink written 6.8 years ago by Raygozak1.2k
5
gravatar for Neilfws
6.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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

ADD COMMENTlink written 6.8 years ago by Neilfws48k
5
gravatar for Flow
6.8 years ago by
Flow1.5k
Flow1.5k wrote:

You should also consider matplotlib

ADD COMMENTlink written 6.8 years ago by Flow1.5k

the library is nice ....

ADD REPLYlink written 6.8 years ago by John1.4k
5
gravatar for Philippe
6.8 years ago by
Philippe1.9k
Barcelona, Spain.
Philippe1.9k wrote:

Hi,

I just dug a bit into my delicious bookmarks and found this few resources.

I hope this helped.

ADD COMMENTlink written 6.8 years ago by Philippe1.9k
4
gravatar for Alastair Kerr
6.8 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

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

Pretty!

ADD COMMENTlink modified 2.9 years ago • written 6.8 years ago by Alastair Kerr5.2k

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

ADD REPLYlink written 6.8 years ago by SES8.1k

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

ADD REPLYlink written 6.8 years ago by John1.4k

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

ADD REPLYlink written 6.8 years ago by Alastair Kerr5.2k
3
gravatar for Ram S
6.8 years ago by
Ram S60
Ram S60 wrote:

Here are some generic ones:

simple graph with r

quick-R

Specialized:

R / heat map plot

R / Manhattan plot

ADD COMMENTlink written 6.8 years ago by Ram S60
3
gravatar for Damian Kao
6.8 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

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

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by Damian Kao15k

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

ADD REPLYlink written 6.8 years ago by Madelaine Gogol5.0k
2
gravatar for Giovanni M Dall'Olio
6.8 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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.

ADD COMMENTlink written 6.8 years ago by Giovanni M Dall'Olio26k
2
gravatar for Yannick Wurm
6.8 years ago by
Yannick Wurm2.3k
Queen Mary University London
Yannick Wurm2.3k wrote:

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.

ADD COMMENTlink written 6.8 years ago by Yannick Wurm2.3k

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

ADD REPLYlink written 6.8 years ago by John1.4k
2
gravatar for Vladimir Chupakhin
6.7 years ago by
Toledo, Spain
Vladimir Chupakhin520 wrote:

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.

ADD COMMENTlink written 6.7 years ago by Vladimir Chupakhin520
1
gravatar for SES
6.8 years ago by
SES8.1k
Vancouver, BC
SES8.1k wrote:

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.

ADD COMMENTlink modified 2.9 years ago • written 6.8 years ago by SES8.1k
1
gravatar for Priyabrata
6.8 years ago by
Priyabrata70
Priyabrata70 wrote:

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/

ADD COMMENTlink written 6.8 years ago by Priyabrata70
1
gravatar for yan1166
2.9 years ago by
yan116610
yan116610 wrote:

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

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

All the best !

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by yan116610
1
gravatar for Collin
2.9 years ago by
Collin630
United States
Collin630 wrote:

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.

ADD COMMENTlink written 2.9 years ago by Collin630
1
gravatar for Manuel Landesfeind
2.9 years ago by
Göttingen, Germany
Manuel Landesfeind1.1k wrote:

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.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Manuel Landesfeind1.1k

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

ADD REPLYlink written 2.9 years ago by Daniel3.7k
0
gravatar for Tyler Davis
6.7 years ago by
Tyler Davis20
Tyler Davis20 wrote:

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

ADD COMMENTlink written 6.7 years ago by Tyler Davis20
0
gravatar for Ibrahim Tanyalcin
2.9 years ago by
Belgium
Ibrahim Tanyalcin880 wrote:

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,

ADD COMMENTlink written 2.9 years ago by Ibrahim Tanyalcin880
0
gravatar for rioualen
2.9 years ago by
rioualen320
France
rioualen320 wrote:

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

ADD COMMENTlink written 2.9 years ago by rioualen320
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