richness <- genome_counts_filt %>%
column_to_rownames(var = "genome") %>%
dplyr::select(where(~ !all(. == 0))) %>%
hilldiv(., q = 0) %>%
t() %>%
as.data.frame() %>%
dplyr::rename(richness = 1) %>%
rownames_to_column(var = "sample")
neutral <- genome_counts_filt %>%
column_to_rownames(var = "genome") %>%
dplyr::select(where(~ !all(. == 0))) %>%
hilldiv(., q = 1) %>%
t() %>%
as.data.frame() %>%
dplyr::rename(neutral = 1) %>%
rownames_to_column(var = "sample")
phylogenetic <- genome_counts_filt %>%
column_to_rownames(var = "genome") %>%
dplyr::select(where(~ !all(. == 0))) %>%
hilldiv(., q = 1, tree = genome_tree) %>%
t() %>%
as.data.frame() %>%
dplyr::rename(phylogenetic = 1) %>%
rownames_to_column(var = "sample")
# Aggregate basal GIFT into elements
dist <- genome_gifts %>%
to.elements(., GIFT_db) %>%
traits2dist(., method = "gower")
functional <- genome_counts_filt %>%
filter(genome %in% labels(dist)[[1]]) %>%
column_to_rownames(var = "genome") %>%
dplyr::select(where(~ !all(. == 0))) %>%
hilldiv(., q = 1, dist = dist) %>%
t() %>%
as.data.frame() %>%
dplyr::rename(functional = 1) %>%
rownames_to_column(var = "sample") %>%
mutate(functional = if_else(is.nan(functional), 1, functional))
# Merge all metrics
alpha_div <- richness %>%
full_join(neutral, by = join_by(sample == sample)) %>%
full_join(phylogenetic, by = join_by(sample == sample)) %>%
full_join(functional, by = join_by(sample == sample))
alpha_div %>%
pivot_longer(-sample, names_to = "metric", values_to = "value") %>%
mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic", "functional"))) %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
ggplot(aes(y = value, x = Bd_status, group=Bd_status, color=Bd_status, fill=Bd_status)) +
geom_boxplot(alpha = 0.5, outlier.shape = NA) +
geom_jitter(width = 0.2, alpha = 0.5) +
facet_wrap(. ~factor(metric, labels=c("richness" = "Richness", "neutral" = "Neutral", "phylogenetic" = "Phylogenetic", "functional"="Functional")), scales = "free", ncol = 5) +
stat_compare_means(show.legend = FALSE) +
coord_cartesian(xlim = c(1, NA)) +
theme_classic() +
theme(
strip.background = element_blank(),
strip.text = element_text(size =12, lineheight = 0.6),
panel.grid.minor.x = element_line(size = .1, color = "grey"),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.text.x = element_blank()
)
