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POR: visualizing p-values in a grid?
 

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  1. POR: visualizing p-values in a grid?
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    <p>So I'm reading two .csv files into dataframes containing gene expression values by brain region. They both look a bit like this:</p> <pre><code> reg1 reg2 reg3 reg4 reg5 reg6 reg6 reg7 reg8 1 0.2036 0.6400 -2.2647 0.5345 0.9812 -0.0390 -1.4486 -0.1340 -1.9157 2 -0.0308 0.2991 -1.8990 0.7063 0.8807 -0.0568 -1.5150 -0.8000 -1.5115 3 -0.0242 0.6358 -2.1675 0.8432 0.8149 -0.0955 -1.3789 -0.2266 -1.5513 4 -0.8990 0.5613 -2.0289 0.8544 1.1060 -0.3846 -1.4800 -0.0717 -1.4325 5 -0.6438 0.8719 -2.2708 0.6790 1.0250 -0.3035 -1.1125 -0.3746 -1.5219 6 -0.7945 0.5943 -1.8478 0.5457 0.7989 -0.1093 -2.3242 0.2995 -1.8066 </code></pre> <p>I'm comparing expression rate by p-value using the following to run t-tests of the genes against each other for each region (the regions are the same in both .csv files).</p> <pre><code>geneA = read.csv("geneA.csv") geneB = read.csv("geneB.csv") test.result = mapply(t.test, geneA, geneB) #store p-values in a column with regions in a separate column: p.values = stack(mapply(function(x, y) t.test(x,y)$p.value, geneA, geneB)) #order p-values ordered = p.values[with(p.values, order(values)),] </code></pre> <p>Now what I'd like to do with these p-values is show them in a map that would look something like this (p-values are made up):</p> <pre><code> geneB reg1 reg2 reg3 reg4 ... reg1 .02 .02 .01 .12 reg2 .03 .03 .05 .02 </code></pre> <p>geneA reg3 .01 .05 .05 .05 reg4 .01 .06 .21 .02 ... and so on and so forth. Any suggestions? Something graphical is preferred. </p>
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