I have made an unimpressively large heatmap in R. The rows correspond to RPKM expression values from GTEx, columns are their tissues.
> heatmap(matrix, Rowv=NA, Colv=NA, col = heat.colors(256), cexRow = 0.5, scale="column")
> dim(matrix) #dimension of my matrix
[1] 18101 53
Does anyone have any ideas as to how to make this more interpretable/cleaner? Or is this kind of data too large for a heatmap? The matrix is
Think about what you want to show. What's the message of the figure ? There's no point having a heatmap (or any other type of figure for that matter) that can't be legibly displayed on standard media (e.g. computer screen or paper). First, if the problem is that there are no patterns to be seen where you expect some, you could consider rescaling the values to try and increase the range that is mapped to colors. However, usually one doesn't want to show individual data points but instead make more general statements about groups so this immediately suggests clustering the data. Also there may be a better representation than the heatmap for what you want to show.