Entering edit mode
10.7 years ago
cheater149
▴
60
Sir, I would like to know what is the major difference between the Domainogram images .I am able to plot the first link,but not able to create the second .what is the major difference in coding that can bring the change.Please help me.
http://ars.els-cdn.com/content/image/1-s2.0-S1046202312001144-gr7.jpg [first link]
http://www.massgeneral.org/cancerresearch/assets/REPIMAGE_HochedlingerFigure%20for%20Konrad.jpg [second link]
Can you explain what type of data you have and how you would like to plot your image (software)? This might help us to answer your question.
the data is a wiggle track file and I used R to plot the image. example: track type=wiggle_0 name="plot" description="chr6:132807183" visibility=full autoScale=on windowingFunction=mean maxHeightPixels=40:40:20 color=0,0,200 priority=10 variableStep chrom=chr6 3004552 0 3053693 0 3076489 2 3093509 0 this is a sample data with which I have worked.
I'd be interested to see what you're using to generate Domainograms, is it the Rscript from Splinter et al. (2012)?
I haven't been able to find the Splinter et al paper, but I would be interested in using the R script from it. Does anyone have a citation or link? Thanks!
Sorry I meant 2011, supp matt includes Rscripts for spider plots / arachnograms and domainograms; it produced A and C in OP's question
the scripts I used are from the following paper. supply data..Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation".
But I couldn't get Splinter data from 2011 paper..
Right you are! I did mean 2012, the group has used these figures in several papers
ya...but what is making the difference..in those images...bcoz the second images are gaining importance as per visualization
Well from a quick glance you should be able to see it has a wider range on the y-axis, i.e. calculates p-values using much larger windows, maybe up to 2^16 bp as opposed to 3 kb in the domainogram Rscript
thank you..I tried increasing the larger window size to the above said size but what I observe is missing of interacting domains and still the image remains the similar way...just a hump at each place..
Thanks for the link!