sankeymien 0.0.2

Sankey diagram for Microbial Enrichment cultures.

Sankey diagram for microbial enrichment culture

Python package to make Sankey diagram for Microbial Enrichment cultures.

Installation

This package requires:

• plotly and kaleido (with google chrome installed).
• pandas and numpy.

It can be installed by cloning this repository and with pip:

pip isntall -e .

Usage

It can be used as a command line:

sankeymien -a abundance_table.tsv -j experiments.json -o testoutput -t taxon

-a abundance_table.tsv is a tabulated file containing as a first column organism ID, several columns corresponding to samples anda column containing taxon name (and given with -t taxon).

-j experiments.json is a json file indicating the experiments and the association between time steps and samples.

-o testoutput is the output folder.

Input

The abundance sample should look like this:

organism	s1	s2	k1	Ec1_1	Ec1_2	Ec1_3	kec1	taxon
org_a	1	2	5	0	0	0	0	Bos
org_b	2000	3000	10	100	120	130	1	Escherichia
org_c	500	600	5	100	200	300	0	Parcubacteria
org_d	20	30	0	25	35	40	0	Methanobacterium

The json should correspond to this:

{
    "experiment_2": {
        "initial": ["s1", "s2"],
        "kit_control": ["k1"],
        "enrichment_T01": ["Ec1_1", "Ec1_2", "Ec1_3"],
        "kit_control_T01": ["kec1"]
    }
}

Output

It generates a Sankey diagram showing the flow of relative abundance of organisms according to the different time steps of the enrichment cultures. The final enrichment is linked to taxon name to show the composition of the final communities.