Question: Heat map generation
0
gravatar for tanni93
3.2 years ago by
tanni9310
United States
tanni9310 wrote:

Hi Biostar community, 

I need to generate a heat map with gene A as the center instead of the common TSS site, and dots extending to left/right of this gene that represent distance from gene B from gene A. How may I do this? I need to generate a heat map very similar to that from the following paper: A LncRNA-MAF:MAFB Transcription Factor Network Regulates Epidermal Differentiation, Figure 5A. I have very minimal programming experience.

Any help is appreciated! I am very new to the Bioinformatics community but very eager to learn!

Thank you in advance!
Tanni

 

 

 

 

rna-seq • 1.4k views
ADD COMMENTlink written 3.2 years ago by tanni9310

I hate being the person saying this but with the information that you provided about your data (none) and the examples of what you did so far (none) it's impossible for us to help.

what are your data? what do you want to show with the heatmap? which language are you using ..R? etc etc.. :)

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by TriS3.6k

Hi TriS,


My project is with motif analysis. I have about 7000 start and end sites for gene A and about 5000 start and end sites for gene B. The goal is to see a distance correlation and I want to generate a heat map like the one I stated in the paper above, except the peak-center will be the distance for gene A and the dots will be how far gene B is from gene A. Yes, I can use R (or other programs if that is recommended). My data consists of two bed/txt/excel files with chromosome number, start site, end site. I will generate this for two different populations.

ADD REPLYlink written 3.2 years ago by tanni9310
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