Chapter 4 Filtered samples

load("data/data.Rdata")
extra_metadata <- read_csv("data/Bombina_microbiome_metadata.csv") %>% 
  rename(animal=sample) %>% 
  rename(sample=EHI_code)

sample_metadata <- sample_metadata %>% 
  left_join(., extra_metadata, by="sample") %>% 
  filter(sample %in% filtered_reads$sample)

genome_counts_filt <- genome_counts_filt %>%
  select(one_of(c("genome",sample_metadata$sample)))%>%
  filter(rowSums(. != 0, na.rm = TRUE) > 0) %>%
  select_if(~!all(. == 0))

genome_metadata <- genome_metadata %>%
  semi_join(., genome_counts_filt, by = "genome") %>%
  arrange(match(genome,genome_counts_filt$genome))

genome_tree <- keep.tip(genome_tree, tip=genome_metadata$genome)

genome_gifts <- genome_gifts[rownames(genome_gifts) %in% genome_counts_filt$genome,]

genome_gifts <- genome_gifts[, colSums(genome_gifts != 0) > 0]

phylum_colors <- read_tsv("https://raw.githubusercontent.com/earthhologenome/EHI_taxonomy_colour/main/ehi_phylum_colors.tsv") %>%
    right_join(genome_metadata, by=join_by(phylum == phylum)) %>%
    arrange(match(genome, genome_tree$tip.label)) %>%
    select(phylum, colors) %>% 
    unique() %>%
    arrange(phylum) %>%
    pull(colors, name=phylum)

save(sample_metadata, 
     genome_metadata, 
     genome_counts_filt, 
     genome_tree,
     genome_gifts, 
     phylum_colors,
     file = "data/data_filtered.Rdata")