hi,here is my problem:
I want to get a heatmap of my samples, so I did it as you described in the analysis example of Costello stool analysis.
These are the commands I used:
read.otu(shared=zy.unique.filter.fn.shared)
heatmap.bin(scale=log2)
then I got this svg file(about 900M)
zy.unique.filter.fn.0.03.heatmap.bin.svg .
However, when I opened it with adobe illustrator, there was nothing.
What is the problem, should I change my graphics software?
You might try opening it in a web browser first. Illustrator seems to do weird things to some of these svg files. Also, if your file is really 900 MB, I suspect Illustrator is very unhappy.
yeah, you are right.
I selected a few samples to generate a smaller heatmap svg file, then it can be visualized in Adobe Illustrator.
However, if I put all my samples together (the number is 48), the heatmap svg file is too large to be visualized in Adobe Illustrator, even in Safari.
I’ wondering if I want all my samples in a heatmap, I need to generate a heatmap of several samples everytime and put them together at last.
How about picking a phylum I’m interested in such as Bacteroides to get a heatmap of all samples? Does this method work out?
Thanks!
yeah, if you increase your otu cutoff the number of otus will drop and you’ll have a more interpretable heatmap. alternatively if you just want to compare the communities then use the heatmap.shared command - the resulting heatmap will be a lower triangular matrix that is 48x48 vs a gazillion by 48