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.
An Interactive Heatmap For Viewing Expression Data Matrices
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.
4 answers
Have you tried Gitools ? You may try the heatmap options provided by Gitools for the visualization of your data.
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Khader Shameer
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)
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 :-)
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.
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Niallhaslam
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