Counts of MAGs per trait

packages <- c("R.utils", "RColorBrewer", "ape", "assertthat", "checkmate",
              "coRdon", "corrplot", "dendextend", "devtools", "doParallel",
              "dplyr", "DT", "factoextra", "formatR", "futile.logger", "ggplot2", 
              "grid", "gtools", "kmed", "lazyeval", "magrittr", "parallel", 
              "pheatmap", "readr", "stringr", "tibble", "tictoc", "tidyr", "vegan")
for (pkg in packages) {
  library(pkg, character.only=TRUE)
}

# bioconductor packages
library(BiocManager)
library(Biostrings)
library(ComplexHeatmap)
library(coRdon)

# everything else
library(gRodon)
library(pairwiseAdonis)
library(EcolUtils)
library(ggtree)
library(microtrait)

load("data/traits.RData")

For each trait, the number of MAGs in which that trait was detected is listed in a data frame. Trait levels (except for GH genes) are separated out into distinct columns for ease of comprehension.

# all traits
bw_all_counts <- sapply(bw_all_traits, function(column) sum(column > 0)) %>% as.data.frame()
bw_all_counts <- bw_all_counts[-1, , drop = FALSE]
colnames(bw_all_counts)[1] <- "Number of MAGs"
bw_all_counts <- bw_all_counts %>% rownames_to_column(var = "Trait name")
bw_all_counts <- bw_all_counts %>%
  separate('Trait name', 
           into = c("Trait level 1", "Trait level 2", "Trait level 3", "Trait level 4",
                    "Trait level 5", "Trait level 6", "Trait level 7"), 
           sep = ":", extra = "merge")

## Warning: Expected 7 pieces. Missing pieces filled with `NA` in 136 rows [1, 2, 3, 4, 5,
## 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

datatable(bw_all_counts)

# transport
bw_transport_counts <- sapply(bw_transport, function(column) sum(column > 0)) %>% as.data.frame()
bw_transport_counts <- bw_transport_counts[-1, , drop = FALSE]
colnames(bw_transport_counts)[1] <- "Number of MAGs"
bw_transport_counts <- bw_transport_counts %>% rownames_to_column(var = "Trait name")
bw_transport_counts <- bw_transport_counts %>%
  separate('Trait name', 
           into = c("Trait level 1", "Trait level 2", "Trait level 3", "Trait level 4",
                    "Trait level 5"), 
           sep = ":", extra = "merge")

## Warning: Expected 5 pieces. Missing pieces filled with `NA` in 1 rows [1].

datatable(bw_transport_counts)

# GH
bw_gh_counts <- sapply(bw_gh, function(column) sum(column > 0)) %>% as.data.frame()
bw_gh_counts <- bw_gh_counts[-1, , drop = FALSE]
colnames(bw_gh_counts)[1] <- "Number of MAGs"
bw_gh_counts <- bw_gh_counts %>% rownames_to_column(var = "GH family")

datatable(bw_gh_counts)