Grouping legend by higher classification, filum and genus? ggplot2-CodePudding

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 try to make something like this

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"))

output

Example data

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

CodePudding user response：

One option to achieve your desired result would be via the ggnewscale package which allows for multiple scales and legends for the same aesthetic.

Put your colors into a named vector which assign a color to each of your Genus
Make a list which of Filums which associated Genuss. To this end I make use of dplyr::distinct and split.

library(ggplot2)
library(ggnewscale)
library(dplyr)

cols <- c("#FC000D", "#30E500", "#E10072", "#730183",
"#B58E2C", "#10A542", "#6C1429",
"#00B9B9", "#E36582", "orange3", "#800009",
"#5E230B", "#CC6187", "#949285", "#FF6A00",
"#FF9D69", "#B08A04", "#005A3F", "#120A5F", "#E7BECD")
cols <- rep_len(cols, length.out = length(levels(d4$Genus)))
names(cols) <- levels(d4$Genus)

groups <- d4 %>% 
  distinct(Filum, Genus) %>% 
  # Add order of Filum and legends
  mutate(order = as.numeric(forcats::fct_inorder(Filum))) %>% 
  split(.$Filum)

For each Filum add a geom_col showing the whole data and a scale_fill_manual where using the limits argument we only show the Genuss associated with this Filum. Doing so all other Genuss will be assigned to NA for which we choose a transparent color.

To get the basic idea of what we are doing here is the code for just two groups:

ggplot(d4)  
  geom_col(aes(x = Pacientes, y=`Relative abundance`, fill = Genus), position = "fill")  
  scale_fill_manual(values = cols, limits = groups$Firmicutes$Genus, na.value = "transparent")  
  new_scale_fill()  
  geom_col(aes(x = Pacientes, y=`Relative abundance`, fill = Genus), position = "fill")  
  scale_fill_manual(values = cols, limits = groups$Bacteroidetes$Genus, na.value = "transparent")

Instead of copying and pasting which becomes cumbersome if we have a lot of groups we could make use of lapply to loop over the groups and add the layers dynamically like so:

  
ggplot(d4)  
  lapply(groups, function(x) {
    list(
      geom_col(aes(x = Pacientes, y=`Relative abundance`, fill = Genus), position = "fill"),
      scale_fill_manual(name = unique(x$Filum),
                        values = cols, limits = x$Genus, na.value = "transparent",
                        guide = guide_legend(order = unique(x$order))),
      new_scale_fill()  
    )
  })  
  scale_x_discrete("Patients")  
  scale_y_continuous("Relative abundance", labels = scales::percent)  
  labs(title = "CAP", subtitle = "Relative abundance of phylum and genus")  
  theme_classic()