Is there a way to make a heatmap using DESeq2 for paired data? I am comparing the lung microbiome with the mouth microbiome in 33 patients And also comparing the lung microbiome over two time points (again paired data).

My OTU table was loaded into R:

otu=import_biom('C:\Users\OneDrive\otu_table.biom')

and my sort of "map" file which just contains SampleID, Location, and Paired. For example:

SampleID  Location   Paired
1_L           Lung           1
1_M          Mouth         1
2_L           Lung           2
2_M          Mouth         2

map=read.csv('C:\Users\OneDrive\Mouth vs lung R map_adj.csv',header=T,row.name=1,stringsAsFactors=F)

Again my data is paired and I want to compare the lung vs the mouth (location) using a heatmap. I've been having trouble with R. And then again with time (baseline vs later) (baseline vs x number of months later).

Thanks!

Not sure what exactly you're looking for, but you can annotate rows and columns of heatmaps to get a visual of how these covariates (location, pair, etc) migrate w/ your clusters.

There are many, many, many packages that provide ways to generate heatmaps. A recent arrival on the scene (~ 1 year old) is the ComplexHeatmap package, which allows you to do pretty much everything you might want with a heatmap. Read through the vignettes to get some inspiration.