GIFTs_elements <- to.elements(genome_gifts_all, GIFT_db) %>%
as.data.frame()
GIFTs_elements_community <- to.community(GIFTs_elements, genome_counts_filt_all %>% column_to_rownames(., "genome") %>% tss(), GIFT_db)
GIFTs_elements_community %>%
as.data.frame() %>%
rownames_to_column(var="sample") %>%
pivot_longer(!sample,names_to="trait",values_to="gift") %>%
left_join(sample_metadata_all, by = join_by(sample == sample)) %>%
mutate(functionid = substr(trait, 1, 3)) %>%
mutate(trait = case_when(
trait %in% GIFT_db$Code_element ~ GIFT_db$Element[match(trait, GIFT_db$Code_element)],
TRUE ~ trait
)) %>%
mutate(functionid = case_when(
functionid %in% GIFT_db$Code_function ~ GIFT_db$Function[match(functionid, GIFT_db$Code_function)],
TRUE ~ functionid
)) %>%
mutate(trait=factor(trait,levels=unique(GIFT_db$Element))) %>%
mutate(functionid=factor(functionid,levels=unique(GIFT_db$Function))) %>%
ggplot(aes(x=sample,y=trait,fill=gift)) +
geom_tile(colour="white", linewidth=0.2)+
scale_fill_gradientn(colours=rev(c("#d53e4f", "#f46d43", "#fdae61", "#fee08b", "#e6f598", "#abdda4", "#ddf1da")))+
facet_grid(functionid ~ species, scales="free",space="free") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
strip.text.y = element_text(angle = 0)) +
labs(y="Traits",x="Samples",fill="GIFT")
