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Old 08-01-2013, 06:20 AM   #9
Location: RTP, NC, USA

Join Date: Jun 2009
Posts: 28

A couple simple things to try that may help:
1. Creating a PDF instead of a JPEG will store a vector based image, which will not be blurry when you zoom in. You do have to adjust the font size accordingly, which for 600 genes makes it extremely small. But if you have to, you can zoom in and read the labels.
2. Run a quick k-means clustering on the data, then draw heatmaps of each cluster separately. I see better results using Kmeans() from the amap package, since it can use correlation as a distance metric. Default R kmeans() does not offer correlation, though you can work around that.

Note that when you make a heatmap in R, or use any function that ultimately calls the R image() function, if you have more rows of data than pixels to display them, the heatmap cells tend to overwrite each other. There is an option "useRaster=TRUE" which creates a rasterized image then uses image resizing to shrink it down. But it works best for data sent to a PDF than onscreen. It also doesn't account for asymmetric matrices, but again you can work around that if you have to.
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