I have a matrix of positive real numbers between 0 and 1; the rows represent genes and columns represent samples. Number of rows is greater than the number of columns by a magnitude of $10^4$. I am wondering how to visualize this in
R. I know heatmap is one of the ways to do this, but are there other ideas. Here are a few points which I want to emphasize in the visualization:
- The rows and columns have no order to them (as you may have already realized); specifically rows and columns are exchangeable.
- The entries of the matrix are positive real numbers between 0 and 1.
- A small fraction of the data (10% of the rows or genes, around 1000) are actually "interesting".
- The matrix represents the estimated probability of genes being more active in a sample.
- I want show: which genes are more active and in which sample. The matrix has a lot of rows in which the probabilities are very similar across columns.
- I am ok with ordering the rows (genes) to make the pattern clearer.
At the moment I can determine active genes in a sample by choosing a cutoff (say $\ge 95\%$) and arrange the genes in such a way that first set of rows are active genes in sample 1, second set of rows are active genes in sample 2, ...
I was also thinking about visualizing a subset of the data, may be by sampling rows. But I did not have any success.
I know these ideas may not be very elegant but rearranges my data in a way which makes the pattern more recognizable.
I know similar questions have been asked before, but I thought my query was a bit more specific, so hopefully I can get better inputs from the members of this forum.