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POR: Which heatmap/image to get row-sorted plot without any dendrogram?
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copied!<p>Which package is best for a <strong>heatmap/image with sorting on rows only, but don't show any dendrogram or other visual clutter (just a 2D colored grid with automatic named labels on both axes)</strong>. I don't need fancy clustering beyond basic numeric sorting. The data is a 39x10 table of numerics in the range (0,0.21) which I want to visualize.</p> <p>I searched SO (see <a href="https://stackoverflow.com/questions/5638462/r-image-of-a-pixel-matrix">this</a>) and the R sites, and tried a few out. Check out <a href="http://rgm2.lab.nig.ac.jp/RGM2/search.php?query=heatmap" rel="nofollow noreferrer">R Graphical Manual</a> to see an excellent searchable list of screenshots and corresponding packages.</p> <p>The range of packages is confusing - which one is the preferred heatmap (like <em>ggplot2</em> is for most other plotting)? Here is what I found out so far:</p> <ul> <li><a href="https://stackoverflow.com/questions/5638462/r-image-of-a-pixel-matrix">base::image</a> - bad, no name labels on axes, no sorting/clustering</li> <li><a href="http://flowingdata.com/2010/01/21/how-to-make-a-heatmap-a-quick-and-easy-solution/" rel="nofollow noreferrer">base::heatmap</a> - options are far less intelligible than the following:</li> <li><a href="http://cran.r-project.org/web/packages/pheatmap/index.html" rel="nofollow noreferrer">pheatmap::pheatmap</a> - fantastic but can't seem to turn off the dendrograms? (any hacks?) </li> <li><a href="http://learnr.wordpress.com/2010/01/26/ggplot2-quick-heatmap-plotting/" rel="nofollow noreferrer">ggplot2 people use geom_tile, as Andrie points out</a></li> <li><a href="http://www.compbiome.com/2010/04/r-heatmaps-with-gplots.html" rel="nofollow noreferrer">gplots::heatmap.2</a> , <a href="http://cran.r-project.org/web/packages/gplots/index.html" rel="nofollow noreferrer">ref</a> - seems to be favored by biotech people, but way overkill for my purposes. (no relation to <em>ggplot*</em> or Prof Wickham)</li> <li><a href="http://rgm2.lab.nig.ac.jp/RGM2/images.php?show=all&query=package:plotrix" rel="nofollow noreferrer">plotrix::color2D.matplot</a> also exists</li> </ul> <p><em><code>base::heatmap</code></em> is annoying, even with args <em><code>heatmap(..., Colv=NA, keep.dendro=FALSE)</code></em> it still plots the unwanted dendrogram on rows.</p> <p>For now I'm going with <em><code>pheatmap(..., cluster_cols=FALSE, cluster_rows=FALSE)</code></em> and manually presorting my table, like this guy: <a href="https://stackoverflow.com/questions/5320814/order-of-rows-in-heatmap">Order of rows in heatmap?</a></p> <p>Addendum: to display the value inside each cell, see: <a href="https://stackoverflow.com/questions/3789549/display-a-matrix-including-the-values-as-a-heatmap">display a matrix, including the values, as a heatmap</a> . I didn't need that but it's nice-to-have.</p>

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