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POplotting heatmaps with ggplot2; logscale color and modify color legend
 

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  1. POplotting heatmaps with ggplot2; logscale color and modify color legend
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    <p>I am trying to create a heatmap with <code>ggplot2</code> (you see the code below) Now there are two things i want to change:</p> <ol> <li>I plot pValues (which are hopefully very small) so i want plot the colors logscale. i tried trans="log" in different variations, but none of them worked</li> <li><p>I want to show more than 6 values in the legend. i tried e.g. breaks, labels for that but this didn't work as well</p> <pre><code>(p &lt;- ggplot(dataPVal.m, aes(variable, structure)) + geom_tile(aes(fill = pValue), colour = "white") + scale_colour_gradientn(colour = rainbow(100), breaks = c(1,2,3,4,5,6), labels =c("a","b","c","d","e","f")) + theme_grey(base_size = base_size) + labs(x = "position (0=seed start)",y = "structure") + ## labels #scale_x_discrete(expand = c(0.01, 0.01)) + ## grauer rand oben/unten #scale_y_discrete(expand = c(0.01, 0.01)) + ## grauer rand links/rechts opts(title=plot_title,legend.position = "left",axis.ticks = theme_blank(), axis.text.x = theme_text(size = base_size * 0.8, angle = 330, hjust = 0, colour = "grey50")) ) </code></pre></li> </ol> <p>here is an example for the pValue-table (dataPVal.m):</p> <pre> structure variable value pValue 1 CB -10 1.00000000 1.00000000 2 BB -10 1.00000000 1.00000000 3 SC -10 0.34700205 0.34700205 4 GC -10 1.00000000 1.00000000 5 BC -10 1.00000000 1.00000000 6 SG -10 0.44494198 0.44494198 7 JG -10 1.00000000 1.00000000 8 IG -10 1.00000000 1.00000000 9 HG -10 1.00000000 1.00000000 10 CG -10 1.00000000 1.00000000 11 HH -10 1.00000000 1.00000000 12 GH -10 0.34375000 0.00000025 13 SI -10 0.25000000 0.25000000 14 JI -10 0.40359735 0.40359735 15 II -10 1.00000000 1.00000000 16 GI -10 1.00000000 1.00000000 17 SJ -10 0.53296021 0.53296021 18 IJ -10 1.00000000 1.00000000 19 GJ -10 1.00000000 1.00000000 20 US -10 0.19567557 0.19567557 21 SS -10 0.43017585 0.00000032 22 JS -10 1.00000000 1.00000000 23 IS -10 1.00000000 1.00000000 24 GS -10 1.00000000 1.00000000 25 CS -10 1.00000000 1.00000000 26 UU -10 0.39863089 0.39863089 27 SU -10 0.50000000 0.50000000 28 JU -10 1.00000000 1.00000000 29 CB -9 0.34944171 0.34944171 30 BB -9 1.00000000 1.00000000 31 SC -9 0.53230531 0.53230531 </pre> <p>is there anybody with a solution for this 2 problems?</p> <p>thx so long</p>
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      1. POplotting heatmaps with ggplot2; logscale color and modify color legend
      1. USRon Gejman
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    1. COhow about showing a sample of the `dataPVal` table?
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      1. POplotting heatmaps with ggplot2; logscale color and modify color legend
      1. USPrasad Chalasani
 

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