Grouping legend by higher classification?

[M_AcostaCH]

HI, Im want make better the legend()

I am looking for the legend to be grouped according to a higher classification (phylum) but that at the same time the genus (Genus) is shown.

I want to have something like that:

Im run this code

ggplot(d4) + 
  geom_bar(aes(x=Pacientes, y=`Relative abundance`,fill=Genus), position="fill", stat="identity") +     scale_x_discrete("Patients") + 
  scale_y_continuous("Relative abundance",labels=scales::percent) +
  labs(title = "CAP",subtitle = "Relative abundance of phylum and genus") +
  theme_classic() + 
  scale_fill_manual(values=c ("#FC000D", "#30E500", "#E10072", "#730183",       "#B58E2C","#10A542","#6C1429",
  "#00B9B9", "#E36582","orange3","#800009",
  "#5E230B","#CC6187","#949285","#FF6A00",
  "#FF9D69","#B08A04","#005A3F","#120A5F","#E7BECD")) 

d4<-structure(list(Pacientes = c("5-006", "5-005", "5-005", "5-001", 
"5-003", "5-002", "5-001", "5-001", "5-005", "5-001", "5-003", 
"5-003", "5-007", "5-006", "5-003", "5-001", "5-002", "5-003", 
"5-002", "5-002", "5-001", "5-002", "5-003", "5-005", "5-002", 
"5-001", "5-006", "5-005", "5-007", "5-005"), Filum = c("Firmicutes", 
"Firmicutes", "Firmicutes", "Firmicutes", "Firmicutes", "Firmicutes", 
"Firmicutes", "Firmicutes", "Proteobacteria", "Proteobacteria", 
"Proteobacteria", "Proteobacteria", "Proteobacteria", "Proteobacteria", 
"Proteobacteria", "Proteobacteria", "Proteobacteria", "Proteobacteria", 
"Spirochaetes", "Spirochaetes", "Spirochaetes", "Spirochaetes", 
"Firmicutes", "Firmicutes", "Bacteroidetes", "Bacteroidetes", 
"Bacteroidetes", "Bacteroidetes", "Bacteroidetes", "Firmicutes"
), Genus = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 12L, 13L, 
13L, 13L, 13L, 13L, 14L, 15L, 15L, 15L, 15L, 20L, 20L, 20L, 20L, 
21L, 21L, 25L, 25L, 25L, 25L, 25L, 26L), .Label = c("Streptococcus", 
"Veillonella", "Haemophilus", "Actinobacillus", "Serratia", "Fusobacterium", 
"Neisseria", "Moraxella", "Abiotrophia", "Granulicatella", "Actinomyces", 
"Oribacterium", "Aggregatibacter", "Escherichia-Shigella", "Lautropia", 
"Geobacillus", "Leptotrichia", "Johnsonella", "Campylobacter", 
"Treponema 2", "Gemella", "Megasphaera", "Atopobium", "Bifidobacterium", 
"Capnocytophaga", "Selenomonas", "Mycoplasma", "Porphyromonas", 
"Alloprevotella", "Lachnoanaerobaculum", "Eikenella", "[Eubacterium] brachy group", 
"Stomatobaculum", "Atopostipes", "Selenomonas 3", "Kingella", 
"Dialister", "F0058", "Parvimonas", "No identificado", "Solobacterium", 
"Otros finales", "Olsenella", "Filifactor", "Rodentibacter", 
"Alloscardovia", "Otros", "[Eubacterium] yurii group", "Anaeroglobus", 
"Staphylococcus", "Ruminococcaceae UCG-014", "Lactobacillus", 
"Rothia", "Selenomonas 4", "Scardovia", "Fluviicola", "Cardiobacterium", 
"Bilophila", "Simonsiella", "[Eubacterium] nodatum group", "Catonella", 
"Peptoniphilus", "uncultured", "Shuttleworthia", "Butyrivibrio 2", 
"Peptostreptococcus", "Mogibacterium", "Bergeyella", "Peptococcus", 
"Faucicola", "Blautia", "Rikenellaceae RC9 gut group", "Eggerthia", 
"Desulfobulbus", "Tannerella", "Lactococcus", "Prevotella", "Otro", 
"Prevotella 7", "Erysipelotrichaceae UCG-006", "Defluviitaleaceae UCG-011", 
"W5053", "Craurococcus", "Dolosigranulum", "Sneathia", "Anaerococcus", 
"Pseudoramibacter", "Family XIII UCG-001", "Ruminococcus 2", 
"Howardella", "Cryptobacterium", "Listeria", "Pantoea", "Akkermansia", 
"Prevotella 6", "Macrococcus", "Paracoccus", "Comamonas", "TM7 phylum sp. oral clone FR058", 
"Peptoanaerobacter", "Rubellimicrobium", "Fastidiosipila", "Brachymonas", 
"Candidatus Tammella", "Slackia", "DNF00809", "Truepera", "Finegoldia", 
"Erysipelotrichaceae UCG-004", "uncultured bacterium", "Bulleidia", 
"Flexilinea", "Methylobacterium", "Propionivibrio", "Ochrobactrum"
), class = "factor"), `Relative abundance` = c(1.797989737427, 
1.17051056033446, 0.967773967968912, 0.890190018788368, 0.875168325944855, 
0.203636768715721, 0.190978038791412, 0.0011814814596022, 0.0411830680204194, 
0.031674955321716, 0.018003527003462, 0.00559797167763897, 0.0032912697803204, 
0.0189880948864639, 0.0386794525465004, 0.0337566131314913, 0.0279054668553661, 
0.0242766309437308, 0.000168783065657456, 0.000112522043771638, 
8.43915328287282e-05, 8.43915328287282e-05, 0.0290306872930825, 
0.0263020277316203, 0.00458527328369423, 0.00393827153200732, 
0.00351631386786368, 0.00210978832071821, 0.000900176350173101, 
0.021744884958869)), row.names = c(NA, -30L), class = c("tbl_df", 
"tbl", "data.frame"))

The grouping colum is Filum and the normal legend is Genus in the data

Thanks

[Matthias]

The microshades package has such a feature ("custom_legend") and offers some colours for microbiome samples.
I started to hijack this for a more generalised approach but for you it should be more easy as the field is similar.
You need 2 files:
-the mdf file (with the data, essential columns: Sample, Abundance, Top_Phylum, Top_Genus)
-the cdf file which contains the colour description (Top_Phylum, Top_Genus, group, hex)
I guess it's also shrinks down the data to the Top5 genus.

Global Patterns Data

[Matthias]

Or you can try this:

r ggplot2: grouping legend in bar plots

[M_AcostaCH]

Im try to do, if I can make, share the results. Thanks.