Heatmap in R - bray curtis

Other Bioinformatics Tools
1

Hi,

I would like to do a heatmap in R where my clustering_distance_rows is based on bray curtis distances. I am using pheatmap.

Anyone knows how to do it?

2

Good place to start, there are a lot of heatmap packages in R. Where you go with it, will depend which package you like. We transitioned from heatmap.2 to pheatmap. Your data or comfort level with R will dictate where you go. Ben

Actually, I realized that we had published some heatmap code. Although, this code takes a QIIME1 biom file, it should be ok if you can upload a QIIME2 biom file into it. Try it here:

1 Like
3

Yes, i am using pheatmap. I was using relative frequencies to do a heatmap but i would like to try to do with bray curtis distances.

1 Like
4

Did you get your answer? Recently, I had the same problem as you when using pheatmap with bray curtis distances.

5

You can try:

`library(vegan)`
`drows = vegdist(test, method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm = FALSE)`

dcols =vegdist(t(test), method="bray", binary=FALSE, diag=FALSE, upper=FALSE, na.rm = FALSE)

then
pheatmap(test, clustering_distance_rows = drows, clustering_distance_cols = dcols)