presenting my bar plots for publication

Any advice please how I can present my bar plots like that

out of something like this

and Is it recommended to filter the low abundance taxa to be able to do this?

I make plots like this using the R packages Phyloseq and ggplot2 + ggpubr. See the Restroom Biogeography example, and search for plot_bar

Yes! In these case they plot these low abundance taxa in a single <1% abundance group.

EDIT: Try the search 'publication quality bar plot' and pick the program you like best. And ask us any questions about how we think about making this common Figure 1 plot. :bar_chart:

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@colinbrislawn Thanks a lot for the guidance.

As this is my first steop into R, can you please share a script with me or share a link to a script where I can start to do my first relative abundance barplots in different test groups in the phylum level as a start?


Thanks a lot.

Good morning,

If you want to make these in R, check out the Phyloseq plot_bar tutorial. You may find qiime2R helpful for importing your data.

I would love to share an example that 'just works, every time!' I find that I have to do some level of processing to my data before I get the graph I want. My process is

  • Import feature, taxonomy, and metadata data into Phyloseq
  • Transform counts into relative abundance
  • Group taxa at a relative abundance level
  • Filter for the most abundant taxa
  • Make a bar plot and add facet_grid(~Treatment)

So the simple method is not complete, and the complete real world code is not simple.

Try some code for yourself and let us know if you have any questions!

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You can use Microbiome analyst, taking OTU generated using Qiime2 ,its online tool.

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