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POCreate a graph/heat map based on a paper
 

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  1. POCreate a graph/heat map based on a paper
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    <p>I want to create a graph like the one in <a href="http://www.google.com/imgres?um=1&amp;hl=el&amp;client=firefox-a&amp;sa=N&amp;rls=org.mozilla%3ael%3aofficial&amp;biw=1600&amp;bih=1108&amp;tbm=isch&amp;tbnid=PD6pwt90NQ9-hM%3a&amp;imgrefurl=http://www.sciencedirect.com/science/article/pii/S0092867411011342&amp;docid=7-5MvR4TgcE9gM&amp;itg=1&amp;imgurl=http://ars.sciencedirect.com/content/image/1-s2.0-S0092867411011342-gr1.jpg&amp;w=468&amp;h=652&amp;ei=UDSRT6nnGcv0-gaT1LD7Aw&amp;zoom=1&amp;iact=hc&amp;vpx=1218&amp;vpy=104&amp;dur=739&amp;hovh=265&amp;hovw=190&amp;tx=104&amp;ty=150&amp;sig=118005667344627929103&amp;page=1&amp;tbnh=114&amp;tbnw=82&amp;start=0&amp;ndsp=71&amp;ved=1t:429,r:8,s:0,i:82" rel="nofollow">this link </a>. I am interested in the graph H (Smad3 and Oct4 co-occupy the genome. For each of the 15,003 Oct4-bound sites (y axis), the presence of Oct4 (blue) and Smad3 (red) are displayed within a 5 kb window centered on each Oct4-bound site.) (adapted from Mellen et al., 2011)</p> <p>For that, I have created a coverage of my chip experiment. I have something like:</p> <pre><code>anna &lt;- Views(anna.cov[[chr]], start=start(experiment.islands),end=end(experiment.islands)) anna start end width [6] 72291 72694 404 [6 6 7 7 7 7 7 7 7 7 7 7 7 7 8 8 8 8 8 ...] [7] 82908 85491 2584 [ 3 3 3 3 3 3 3 3 3 3 3 3 4 ...] [8] 90902 91101 200 [6 6 6 6 6 6 6 6 7 7 7 7 7 6 6 6 6 7 7 ...] [9] 95272 95331 60 [6 6 6 6 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 ...] </code></pre> <p>Now what should I do?</p>
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    1. USAnna
    1. USAnna
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    1. COMight I suggest that you go back to some of your previous questions and accept peoples' solutions? People here are often willing to sacrifice their time to help others, and you can encourage such behaviour by showing appreciation through accepting a useful solution. It also indicates that your issue has been resolved (and, by looking at your previous questions, it seems many were).
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      1. POCreate a graph/heat map based on a paper
      1. USjbaums
    2. COsorry about that....i am new in this world...i did already what you asked
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      1. USAnna
    3. COI'm unclear on your R data. Can you include the code for how to generate a sample of that data as an R variable? Given that, someone may be able to come up with a good way to plot it.
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      1. POCreate a graph/heat map based on a paper
      1. USJeff Allen
 

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