how to present the data by a stack chart for different treatments with several replicates (in each treatment)

Question

[flavobacteria]

As you know, we generally have several replicates (for example, we sequence 5 samples for each treatment), we have these output (e.g. we get their relative abundance). What do you suggest for a stack bar chart if we try to compare different treatments in one figure (I mean how to deal these replicates)? Thanks

[Selenocysteine]

I am not sure if I understood the question correctly, but since you have different replicates for each condition I would go for a boxplot like in this example taken from the internet:

(you can use the ggplot2 library in R). In this example, group 1 would be your treatment 1, group 2 your treatment 2, etc.

Indeed, in my opinion stacked box plot are not really a good idea for representing any data, let alone data based on multiple replicates.

Answer 1

[flavobacteria]

This figure I want to create for 16s rDNA analysis. It is quite a busy figure if I plot several samples with different OTUs (even I chose top 20) and I have some many replicates. It will be a stack bar chart---see this paper.

But they combine their replicates in one.

Anyway, can anyone gives some advice how to compare their OTUs at higher taxonomy level (they use family and class levels). I have a Figure (relative abundance at the genus level). Thank you!