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Blog by Michael Roach: @BeardyMcJohnFace@genomic.social
email: mroach@bioinf.cc

Krona plots are easy (metagenomics example)

21 Feb 2022

Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of all they're surprisingly easy to make. We'll use output from the metagenomics profiler 'FOCUS' as an example.

FOCUS is an excellent tool for profiling the microbial communities of metagenomics samples, and its spiritual successor SuperFOCUS extends the tool to include subsystem-level profiling. This example will use a small output file: focusOutputEg.csv.zst

A quick look at this file shows columns 1-8 contain the taxonomic annotation, and columns 9 and 10 contain the percentage of R1 and R2 reads that match this annotation. BTW, if you’re not using zstandard, you should try it out. It has fast, parallel, decent file compression, and it has blazingly fast decompression–almost as fast as lz4.

$ zstdcat focusOutputEg.csv.zst | head
Kingdom,Phylum,Class,Order,Family,Genus,Species,Strain,ERR1467153_R1.fastq,ERR1467153_R2.fastq
Bacteria,Proteobacteria,Alphaproteobacteria,Rhodospirillales,Rhodospirillaceae,Rhodospirillum,Rhodospirillum_photometricum,Rhodospirillum_photometricum_uid159003,0.0,0.30543199636450163
Archaea,Euryarchaeota,Halobacteria,Halobacteriales,Halobacteriaceae,Natronobacterium,Natronobacterium_gregoryi,Natronobacterium_gregoryi_SP2_uid74439,0.12957821822784493,0.0805041736315925
Bacteria,Proteobacteria,Deltaproteobacteria,Desulfobacterales,Desulfobacteraceae,Desulfatibacillum,Desulfatibacillum_alkenivorans,Desulfatibacillum_alkenivorans_AK_01_uid58913,0.4362273642891679,0.2723663810922735
Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Acidovorax,Acidovorax_sp._JS42,Acidovorax_JS42_uid58427,1.774572695525898,2.832211940191908
Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Bradyrhizobiaceae,Rhodopseudomonas,Rhodopseudomonas_palustris,Rhodopseudomonas_palustris_BisA53_uid58445,0.0,0.16279122445280586
Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Clostridium,[Clostridium]_difficile,Clostridium_difficile_CF5_uid158359,0.05616259811855688,0.07011765537568315
Bacteria,Proteobacteria,Deltaproteobacteria,Myxococcales,Myxococcaceae,Corallococcus,Corallococcus_coralloides,Corallococcus_coralloides_DSM_2259_uid157997,0.0,0.03792781030247689
Bacteria,Proteobacteria,Gammaproteobacteria,Enterobacteriales,Enterobacteriaceae,Enterobacter,Enterobacter_sp._R4-368,Enterobacter_R4_368_uid208672,0.13149443908001496,0.0
Bacteria,Firmicutes,Clostridia,Clostridiales,Eubacteriaceae,Eubacterium,Eubacterium_eligens,Eubacterium_eligens_ATCC_27750_uid59171,0.5336824177251188,0.8448355470993689

For Krona, we want to use the text input file format. We will remove the header, have the count (sum of the R1 and R2 percent) for each line as the first column, and have tab-separated fields for the taxonomic annotations. We can do this with a bash command:

zstdcat focusOutputEg.csv.zst \
  | tail -n+2 \
  | awk -F ',' '{n=$9+$10; print n"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8}' \
  > focusKronaText.tsv

And look at our lovely new file:

$ head focusKronaText.tsv 
305432	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Rhodospirillaceae	Rhodospirillum	Rhodospirillum_photometricum	Rhodospirillum_photometricum_uid159003
210082	Archaea	Euryarchaeota	Halobacteria	Halobacteriales	Halobacteriaceae	Natronobacterium	Natronobacterium_gregoryi	Natronobacterium_gregoryi_SP2_uid74439
708594	Bacteria	Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	Desulfatibacillum	Desulfatibacillum_alkenivorans	Desulfatibacillum_alkenivorans_AK_01_uid58913
60678	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	Acidovorax	Acidovorax_sp._JS42	Acidovorax_JS42_uid58427
162791	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Bradyrhizobiaceae	Rhodopseudomonas	Rhodopseudomonas_palustris	Rhodopseudomonas_palustris_BisA53_uid58445
12628	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	Clostridium	[Clostridium]_difficile	Clostridium_difficile_CF5_uid158359
0379278	Bacteria	Proteobacteria	Deltaproteobacteria	Myxococcales	Myxococcaceae	Corallococcus	Corallococcus_coralloides	Corallococcus_coralloides_DSM_2259_uid157997
131494	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter	Enterobacter_sp._R4-368	Enterobacter_R4_368_uid208672
37852	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium	Eubacterium_eligens	Eubacterium_eligens_ATCC_27750_uid59171
0158	Bacteria	Proteobacteria	Betaproteobacteria	Methylophilales	Methylophilaceae	Methylotenera	Methylotenera_versatilis	Methylotenera_301_uid49469

Install KronaTools if you haven’t already using conda:

conda install -c bioconda krona

Run Krona. There are many KronaTools commands, but we’ll use ktImportText for converting out text input format into a Krona plot. The command is very simple:

ktImportText focusKronaText.tsv -o focusKrona.html

You can now open the .html file and explore your data. Double click to expand, back arrows to go back, download SVG snapshots for your publications and presentations!