Alignment of Communities with Different Functional Types

library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(fsmc)
library(magrittr)
library(purrr)
#> 
#> Attaching package: 'purrr'
#> The following object is masked from 'package:magrittr':
#> 
#>     set_names
library(readr)
library(stringr)
library(tidyr)
#> 
#> Attaching package: 'tidyr'
#> The following object is masked from 'package:magrittr':
#> 
#>     extract

selection <- c(“A1R12”, “B3M02”, “3D05”) facilitation <- c(“E3M17”, “D2R05”, “E3R18”)

Load Data

ft_url <- "https://raw.githubusercontent.com/admarhi/fsmc-data/main/misosoup/func_type.csv"

ft_tb <- 
  read_csv(ft_url) %>% 
  group_by(func_type, substrate, focal_strain) %>% 
  filter(solution <= 2) %>% 
  ungroup() %>%
  nest(.by = c("func_type", "substrate", "focal_strain", "solution")) %>% 
  mutate(name = paste(substrate, focal_strain, solution, sep = "_"))
#> Rows: 76606 Columns: 7
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (5): func_type, substrate, focal_strain, species, metabolite
#> dbl (2): solution, flux
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

selection_tb <- ft_tb %>% 
  filter(func_type == "selection")

selection <- 
  set_names(selection_tb$data, selection_tb$name) %>% 
  imap(newMiCo)

facilitation_tb <- ft_tb %>% 
  filter(func_type == "facilitation")

facilitation <- 
  set_names(facilitation_tb$data, facilitation_tb$name) %>% 
  imap(newMiCo)

selection_alig <- newMiCoAl(selection)
facilitation_alig <- newMiCoAl(facilitation)

plotAlignmentHeatmap(selection_alig, 0.5)

plotAlignmentHeatmap(facilitation_alig, 0.5)

plotAlignmentHeatmap(selection_alig, 0.8)

plotAlignmentHeatmap(facilitation_alig, 0.8)

plotAlignmentHeatmap(selection_alig, 0.95)
#> [1] "No Alignment at this level."
plotAlignmentHeatmap(facilitation_alig, 0.95)

plotAlignmentNetwork(selection_alig, 0.5)

plotAlignmentNetwork(facilitation_alig, 0.5)

plotAlignmentNetwork(selection_alig, 0.8)

plotAlignmentNetwork(facilitation_alig, 0.8)

plotAlignmentNetwork(selection_alig, 0.95)

plotAlignmentNetwork(facilitation_alig, 0.95)