Question: An Interactive Heatmap For Viewing Expression Data Matrices
10
gravatar for Qdjm
8.4 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

I have a matrix of expression data (rows -- genes, cols -- samples) that I want to view as a heatmap. It has row and column labels. And I want to be able to interactively sort the rows by expression in any one column (or alphabetically by column), or the columns by expression in any one row.

Basically, a paired down version of Excel, but with colours instead of numbers and a one-click sort interface.

Oh, one more thing, the matrix isn't that big -- maybe at most ~100 genes and ~50 samples and usually smaller.

Among the plethora of bioinformatics webservers and tools, there's got to be something that does this, any ideas?

Please don't answer "do it in MATLAB", or R, or whatever, I can do that but I want something with a bit less hassle -- ideally, I upload my tab-delimited textfile to some craftily designed website.

ADD COMMENTlink modified 8.2 years ago by Niallhaslam2.2k • written 8.4 years ago by Qdjm1.9k
10
gravatar for Khader Shameer
8.4 years ago by
Manhattan, NY
Khader Shameer17k wrote:

Have you tried Gitools ? You may try the heatmap options provided by Gitools for the visualization of your data.

ADD COMMENTlink written 8.4 years ago by Khader Shameer17k

Looks like a very cool tool. The interface is a little unintuitive. It took me a bit of time to figure out where the "heatmap" option was. It was a bit hard to figure out how to load my own data into the interface. Perhaps it would have been easier if I read the instructions (or watched the tutorial) or if I wasn't using the Java webstart. But I did manage to find the heatmap option, though I could only sort by columns, not rows.

ADD REPLYlink written 8.4 years ago by Qdjm1.9k

sorting can be done for rows, columns and both at a time if you access the "Data->Sort->By Value" Dialog. Hope this helps

ADD REPLYlink written 8.3 years ago by Michi940

dmeu: Thanks for the tip !

ADD REPLYlink written 8.2 years ago by Khader Shameer17k
4
gravatar for Mary
8.4 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Have you explored this tool at all? Expression Profiler at EBI.

http://www.ebi.ac.uk/expressionprofiler/

(we're checking other tools we know about too--may have other suggestions later)

ADD COMMENTlink written 8.4 years ago by Mary11k

Just tried it, it's not a bad tool -- maybe a little slow for me -- but I wasn't able to get it to do what I want to be able to do. I couldn't easily figure out how to sort by row/col expression but it does make a nice clustering diagram.

ADD REPLYlink written 8.4 years ago by Qdjm1.9k

Thanks by the way!

ADD REPLYlink written 8.4 years ago by Qdjm1.9k
3
gravatar for Neilfws
8.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

I have not tried GeneMESH (requires registration), but the article abstract states that: "Expression intensity values of groups of genes that cluster in relation to a given MeSH category, gene ontology or pathway can be displayed as heat maps of Z score-normalized values."

If you can do it in R, why is it hassle? Just save the code and you'll have it forever. Sometimes a little time invested now saves time later :-)

ADD COMMENTlink written 8.4 years ago by Neilfws48k

Thanks for the suggestion but I can't sort by rows or columns. I suppose I could make a little tool in R but I'm sure someone else has already done this, so I'm going to wait to see more answers.

ADD REPLYlink written 8.4 years ago by Qdjm1.9k

GeneMESH doesn't seem to allow you to sort by rows or columns.

ADD REPLYlink written 8.4 years ago by Qdjm1.9k
2
gravatar for Niallhaslam
7.9 years ago by
Niallhaslam2.2k
Dublin
Niallhaslam2.2k wrote:

If you want nice and you want it on the web then i would recommend Protovis:

http://vis.stanford.edu/protovis/ex/heatmap.html

You may have to play around with the data table - but it isn't too hard to get it into the right format for protoviz.

ADD COMMENTlink written 7.9 years ago by Niallhaslam2.2k
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