Demo data

In this vignette, several of mako’s functions will briefly be introduced with an example data set consisting of only 5 taxa and 20 samples. This data set is simple enough that most relevant nodes can be visualized in Neo4j Browser, making it feasible to follow along with all of mako’s operations.

The tables below give an overview of the data contained in the BIOM file.

Download the files here:
demo.biom
demo_1.graphml
demo_2.graphml

Count table:

OTUSample1Sample2Sample20
OTU_1006
OTU_2511
OTU_3000
OTU_4210
OTU_5010

Taxonomy table:

OTUPhylumClassOrderFamilyGenusSpecies
OTU_1ProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceEscherichia
OTU_2FirmicutesClostridiaHalanaerobialesHalobacteroidaceaeSporohalobacterlortetii
OTU_3EuryarchaeotaMethanomicrobiaMethanosarcinalesMethanosarcinaceaeMethanosarcina
OTU_4FirmicutesClostridiaHalanaerobialesHalanaerobiaceaeHalanaerobiumsaccharolyticum
OTU_5ProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceEscherichia

Sample metadata (BarcodeSequence and LinkerPrimerSequence not shown):

SampleBODY_SITEDescription
Sample1-10guthuman gut
Sample11-20skinhuman skin

Edge list:

NetworkTargetSourceWeight
demo_1OTU_1OTU_21
demo_1OTU_2OTU_51
demo_1OTU_3OTU_4-1
demo_1OTU_1OTU_51
demo_2OTU_1OTU_21
demo_2OTU_2OTU_51
demo_2OTU_1OTU_5-1