Taxonomic Barplot for visualising MetaPhlAn3 outcome

Microbial community profiling MetaPhlAn
1

Hi
I used MetaPhlAn3 for the classification but now I want to make Taxonomic bar plots for my samples. In the MetaPhlAn3 tutorial I could find only the heatmaps and cladograms using the graphlan. Is there any options available to visualise the abundance of samples suing the bar plots?

Thanks
Saraswati Awasthi
@fbeghini

2

Have you considered looking at ggplot2 or matplotlib for plotting the data?

3

Thanks for your response, I never have tried using GGPLOT2 or MATPLOTLIB but thanks for the suggestion.

4

Hi @fbeghini

I have few Doubts:

  • Taxa Bar Plots using Biobakery Workflows:

I was going through the biobakery workflows, I found that I can get the taxonomic barplot chart for comparing all the samples through the biobakery workflow. But Biobakery workflow uses MetaPhlAn2 and so is it possible to viral diversity too through the workflow?
My goal is to get a stacked Bar Chart to compare all the samples where in each Stacked bar the sames species should be represented by the same colour. But I have a problem that each sample has some percentage of

  1. Bacteria
  2. Viral
  3. Eukaryotes
    So I have to make separate charts for Bacteria, then separate for Virus and another chart for eukaryotes and I want to get 100% weightage to each category.
  • MetaPhlAn3 gives unclassified viruses:
    After adding the --add_viruses flag I got some percentage of viral species but how, for most of the viral result, does it classifiy directly to the species level and not the genus,family,order,class as they remain unclassifed?
    This is what I got:
    k__Viruses|p__Viruses_unclassified|c__Viruses_unclassified|o__Caudovirales|f__Siphoviridae|g__Siphoviridae_unclassified|s__Microbacterium_phage_Min1 10239|||28883|10699||446529 0.61931
    k__Viruses|p__Viruses_unclassified|c__Viruses_unclassified|o__Caudovirales|f__Siphoviridae|g__Siphoviridae_unclassified|s__Microbacterium_phage_Min1 10239|||28883|10699||446529 0.61931
    k__Viruses|p__Viruses_unclassified|c__Viruses_unclassified|o__Viruses_unclassified|f__Viruses_unclassified|g__Viruses_unclassified|s__Pseudomonas_phage_PA16 10239||||||347331 0.39614

Thank You
Saraswati