Question: Heat Map Of Pan-Genome
2
gravatar for Robert Jenkins
8.7 years ago by
Robert Jenkins120 wrote:

Hi I have constructed a pan-genome using reciprocal blast hits(RBH) of 5 species genome.As expected the pan-genome contains the core genes(shared/conserved in all species),partially shared genes (shared/conserved between two or more species but not all) and unique genes(found in single specie).Now I am trying to visualize the obtained distribution of genes(core,partially shared and unique) onto a heat map.I tried many freely available resources for generating heat map but most of them deal with displaying microarray/expression data therefore I request suggestions which deal in generating heat map of pan-genome. Thanks Robert

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ADD COMMENTlink written 8.7 years ago by Robert Jenkins120
4
gravatar for Madelaine Gogol
8.7 years ago by
Madelaine Gogol5.2k
Kansas City
Madelaine Gogol5.2k wrote:

Maybe you could try MeV?

ADD COMMENTlink written 8.7 years ago by Madelaine Gogol5.2k

MeV is right choice of GUI based statistical inference visualization and it does what I had asked....Thanks Madelaine,However following earlier advice I learnt a bit of R and find it more versatile to draw what I wanted.

ADD REPLYlink written 8.7 years ago by Robert Jenkins120

MeV is right choice for GUI based statistical inference visualization and it does what I had asked....Thanks Madelaine,However following earlier advice I learnt a bit of R and find it more versatile to draw what I wanted.

ADD REPLYlink written 8.7 years ago by Robert Jenkins120
1
gravatar for Gmoney
8.7 years ago by
Gmoney220
Gmoney220 wrote:

R is great for these sorts of visualizations. You won't have to learn too much. My preferred R gui is R Studio, which is great for novices.

This one seems very nice and straightforward: http://flowingdata.com/2010/01/21/how-to-make-a-heatmap-a-quick-and-easy-solution/

My leaning is for MeV for quick and dirty things, as Madelaine recommended. It's quick to get to the result, and offers some nice ways to reslice the data.

ADD COMMENTlink written 8.7 years ago by Gmoney220

Nice and simple example to draw heat map using R.It gave me the basic idea of hot to use R packages and function.Now I can even draw the dendodram which I had appended previously, using heatmap.2 function.I feel R is the best option which utilizes statistical methods to draw conclusions

ADD REPLYlink written 8.7 years ago by Robert Jenkins120

Nice and simple example to draw heat map using R.It gave me the basic idea of how to use R packages and function.Now I can even draw the dendodram which I had appended previously, using heatmap.2 function.I feel R is the best option which utilizes statistical methods to draw conclusions – Robert jenkins 0 secs ago

ADD REPLYlink written 8.7 years ago by Robert Jenkins120
0
gravatar for Gustavo
8.7 years ago by
Gustavo530
Seattle
Gustavo530 wrote:

The most generic tool I can think of is... Excel. One can use the "Conditional Formatting" feature to select a table and paint it dynamically according to cell contents.

I imagine in your case you'd have one row per gene (sorted according to what? position in the human genome?) and one column per species. This would yield a very long matrix - perhaps not the most amenable to plotting as a heatmap, unless you break it into segments and lay these out side by side. Nevertheless, in Excel it will be trivial to make the columns wide enough, and by zooming the spreadsheet out you can get a reasonable heatmap very easily.

Conditional formatting is a bit clumsy in version 2008 of office, but by version 2011 it's actually quite powerful.

ADD COMMENTlink written 8.7 years ago by Gustavo530

Thanks Gustavo.Yes it did worked using conditional formatting coloring scheme and divided the overall data into subsets according to their presence and absence.However Now I want to move a further step and introduce the hierarchical clustering on the normalized value I have and draw a dendogram.There is specialized package which integrates all these steps in R called gplots but I'm really naive to write the codes in R therefore looking for some web based GUI to upload the my file for the desires visualization?

ADD REPLYlink written 8.7 years ago by Robert Jenkins120

Thanks Gustavo.Yes it did work using conditional formatting coloring scheme and I also divided the overall data into subsets according to the gene presence and absence.However Now I want to move a further step to introduce hierarchical clustering on the normalized value and draw a dendogram.There is specialized package which integrates all these steps in R called gplots but I'm really naive to write the codes in R therefore looking for some web based GUI to upload the file for the desires visualization?

ADD REPLYlink written 8.7 years ago by Robert Jenkins120
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