FishTaco file formats

Taxa abundance file

A tab-delimited text file (with headers), where each row is a taxon and each column is a sample, and each cell represents the relative abundance of the taxon in the sample:

Taxa	Sample1	Sample2	Sample3
Taxon1	0.2	0.5	0.1
Taxon2	0.3	0.1	0.7
Taxon3	0.3	0.2	0.1
Taxon4	0.2	0.2	0.1

Function abundance file

A tab-delimited text file (with headers), where each row is a function (e.g., KO) and each column is a sample, and each cell represents the relative abundance of the function in the sample:

Function	Sample1	Sample2	Sample3
K00001	0.1	0.1	0.1
K00002	0.3	0.1	0.1
K00003	0.1	0.1	0.2
K00004	0.2	0.1	0.2
K00005	0.2	0.1	0.2
K00006	0.1	0.5	0.2

Sample sets labels file

A tab-delimited text file (with headers), with two columns, where each row is a sample the value is the sample label:

Sample	Label
Sample1	1
Sample2	0
Sample3	1

Genomic content file

A tab-delimited text file (with headers), where each row is a taxon and each column is a function, and each cell represents the copy number of the function in the genome of the taxon:

Taxa	K00001	K00002	K00003	K00004	K00005	K00006
Taxon1	1	2	0	1	2	0
Taxon2	0	3	0	1	0	0
Taxon3	2	1	2	2	3	1
Taxon4	0	0	2	0	3	2

FishTaco output file (*_main_output_*)

A tab-delimited text file (with headers), where each row is a taxon and each column is a function, and each cell represents the mode and value of contribution to the observed functional shift:

Taxa	K00001	K00002	K00003	K00004	K00005	K00006
Taxon1	a:0.038	a:0.4	c:0.01	c:0.34	b:-0.004	d:-0.01
Taxon2	c:0.293	b:-0.03	d:-0.002	c:0.003	a:0.0631	a:0.2139
Taxon3	b:-0.008	b:-0.015	a:0.03	c:0.0008	d:-0.009	d:-0.011
Taxon4	a:0.048	d:-0.061	b:-0.004	a:0.019	c:4.996	c:0.045

a: case-associated taxon driving enrichment of function in cases; b: case-associated taxon attenuating enrichment of function in cases; c: control-associated taxon driving enrichment of function in cases; d: control-associated taxon attenuating enrichment of function in cases;

FishTacoPlot taxonomy file (for visualization)

In order to plot FishTaco’s decomposition of functional shifts into taxon-level contributions, a taxonomy file linking the various taxa to their phylogenetic assignment is required. The taxonomy file is a tab-delimited text file with no headers, where each row represents one taxon. The format is the taxon name (matching the names in the taxonomic abundance file), followed by its assignment to the following phylogenetic levels: ‘kingdom’,’phylum’,’class’,’order’,’family’,’genus’,’species’, all prefixed by the first letter of the level followed by 2 underscores. Here is an example of the first 5 rows of the default taxonomy file used by the FishTacoPlot package:

Abiotrophia defectiva	k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Aerococcaceae	g__Abiotrophia	s__defectiva
Acaryochloris marina	k__Bacteria	p__Cyanobacteria	c__Cyanophyceae	o__Synechococcales	f__Acaryochloridaceae	g__Acaryochloris	s__marina
Acetivibrio cellulolyticus	k__Bacteria	p__Firmicutes	c__Clostridia	o__Clostridiales	f__Clostridiaceae	g__Acetivibrio	s__cellulolyticus
Acetobacter pasteurianus	k__Bacteria	p__Proteobacteria	c__Alphaproteobacteria	o__Rhodospirillales	f__Acetobacteraceae	g__Acetobacter	s__pasteurianus
Acetohalobium arabaticum	k__Bacteria	p__Firmicutes	c__Clostridia	o__Halanaerobiales	f__Halobacteroidaceae	g__Acetohalobium	s__arabaticum