Example Workflow
example_workflow.RmdThis vignette outlines an exemplary workflow for the
fsmc package. The workflow will be broken down into the
following steps:
- Community object creation
- Community alignment
- Analysis of the alignment
Create a MiCo Object
fsmc contains a set of example data that can be used for
the analysis of microbial communities. For this example, we will use
data created by MiSoS(oup). Two example
communities are provided in the package ac_A1R12_1 and
cit_A1R12_1.
The MiCo function can take either a path to a .csv file
or a data frame/tibble as input.
# Inspect the data
ac_A1R12_1
#> metabolites species fluxes
#> 1 ac A1R12 0.77292503
#> 2 ac I2R16 -10.76733455
#> 3 acald A1R12 -1.12096390
#> 4 acald I2R16 1.12096390
#> 5 ala__D A1R12 0.76031357
#> 6 ala__D I2R16 -0.76031357
#> 7 ala__L A1R12 1.21684157
#> 8 ala__L I2R16 -1.21684157
#> 9 asp__L A1R12 -0.58268031
#> 10 asp__L I2R16 0.58268031
#> 11 co2 A1R12 0.61840930
#> 12 co2 I2R16 12.12608512
#> 13 etoh A1R12 -0.18475279
#> 14 etoh I2R16 0.18475279
#> 15 glu__L A1R12 0.50682546
#> 16 glu__L I2R16 -0.50682546
#> 17 gly A1R12 -0.02158742
#> 18 gly I2R16 0.02158742
#> 19 gthox A1R12 1.45273848
#> 20 gthox I2R16 -1.45273848
#> 21 gthrd A1R12 -2.90547696
#> 22 gthrd I2R16 2.90547696
#> 23 h2o2 A1R12 -1.45273848
#> 24 h2o2 I2R16 1.45273848
#> 25 h2s A1R12 -0.00238294
#> 26 h2s I2R16 0.00238294
#> 27 pyr A1R12 -2.01918234
#> 28 pyr I2R16 2.01918234
cit_A1R12_1
#> metabolites species fluxes
#> 1 ac A1R12 10.072387832
#> 2 ac m_1A01 -10.072387832
#> 3 acald A1R12 8.313282235
#> 4 acald m_1A01 -8.313282235
#> 5 ala__D A1R12 1.296902243
#> 6 ala__D m_1A01 -1.296902243
#> 7 ala__L A1R12 1.895352540
#> 8 ala__L m_1A01 -1.895352540
#> 9 arg__L A1R12 -0.002864506
#> 10 arg__L m_1A01 0.002864506
#> 11 asp__L A1R12 -1.208257612
#> 12 asp__L m_1A01 1.208257612
#> 13 cit A1R12 -9.984232514
#> 14 cit m_1A01 -0.015767486
#> 15 co2 A1R12 5.025755125
#> 16 co2 m_1A01 11.498625545
#> 17 etoh A1R12 -10.022199622
#> 18 etoh m_1A01 10.022199622
#> 19 glu__L A1R12 1.144004523
#> 20 glu__L m_1A01 -1.144004523
#> 21 gly A1R12 -1.094858850
#> 22 gly m_1A01 1.094858850
#> 23 h2s A1R12 0.248451996
#> 24 h2s m_1A01 -0.248451996
#> 25 ile__L A1R12 0.293347327
#> 26 ile__L m_1A01 -0.293347327
#> 27 leu__L A1R12 0.454901455
#> 28 leu__L m_1A01 -0.454901455
#> 29 pyr A1R12 -5.293129303
#> 30 pyr m_1A01 5.293129303
#> 31 ser__L A1R12 -0.003532705
#> 32 ser__L m_1A01 0.003532705
#> 33 succ A1R12 9.984081286
#> 34 succ m_1A01 -9.984081286
#> 35 thr__L A1R12 -0.297725162
#> 36 thr__L m_1A01 0.297725162
#> 37 val__L A1R12 0.427848544
#> 38 val__L m_1A01 -0.427848544
# Create MiCo objects
mc1 <- newMiCo(ac_A1R12_1)
mc2 <- newMiCo(cit_A1R12_1)
mc3 <- newMiCo(ac_A1R12_2)
mc4 <- newMiCo(cit_A1R12_2)
# Inspect MiCo Objects
mc1
#> ac_A1R12_1: MiCo (MicrobialCommunity) Object
#> - Unique microorganisms (MO): 2
#> - Unique metabolites (met): 14
mc1
#> ac_A1R12_1: MiCo (MicrobialCommunity) Object
#> - Unique microorganisms (MO): 2
#> - Unique metabolites (met): 14Align MiCo Objects
Two MiCo objects can be aligned by creating a
MiCoAl object. The MiCoAl creator function can
take any number of MiCo objects as input.
# Align the MiCo objects by creating a MiCoAl object
alignment <- newMiCoAl(mc1, mc2, mc3, mc4)
# Inspect the alignment
alignment
#> Microbial Community Alignment Object (MiCoAl)
#> Alignment of 4 communities with an overall score of ### ToDo ###.