Hello everybody. I am making a phylogenetic tree but when I add the bootstrap values I get some greater than 100. I leave you the code I am using:
library(ggtree)
library(viridis)
library(gdata)
library(dplyr)
library(readxl)
library(ggplot2)
library(ggnewscale)
library(gplots)
library(paletteer)
library(scales)
library(ape)
arbol_seg_s <- read.tree("arbol_segmento_s_ref_SN.fa.treefile")
# Enraizar el árbol en un nodo específico (por ejemplo, en la raíz)
arbol_enraizado <- root(arbol_seg_s, outgroup = "L37904.1")
datos <- read_excel("metadata_segmento_S_sn.xlsx")
Pais <- data.frame("Pais" = factor(datos$Pais))
Año <- data.frame("Año" = factor(datos$Año))
rownames(Pais) <- datos$ID_nuevo
rownames(Año) <- datos$ID_nuevo
arbol_enraizado$tip.label <- datos$ID_nuevo
p1 <- ggtree(arbol_enraizado, layout = 'rectangular') +
geom_tiplab(size = 2.0) +
geom_text2(aes(subset = !isTip, label = as.numeric(node.labels)), hjust = -0.3) +
theme(
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank(),
plot.title = element_text(
size = 15,
face = "bold",
hjust = 0.9,
vjust = -15
)
)
p1 <- p1 + theme(plot.margin = margin(0, 0, 0, 0, "cm")) # Ajustar según necesidades
p2 <- gheatmap(p1, Pais,
offset = 0.01,
width = 0.20,
color = NULL,
colnames = FALSE) +
scale_fill_manual(name = "Pais",
values = c("chile" = alpha("#5499C7", 0.5), # Ajustar transparencia con alpha
"argentina" = alpha("#A569BD", 0.5)), # Ajustar transparencia con alpha
breaks = c("chile", "argentina"),
labels = c("Chile", "Argentina")) +
theme(legend.position = "right",
legend.title = element_text(size = 12),
legend.text = element_text(size = 12),
legend.box = "vertical",
legend.margin = margin()) +
guides(fill = guide_legend(keywidth = 0.7, keyheight = 0.7)) # Ajusta keywidth según tus necesidades
p3 <- p2 + new_scale_fill()
print(p3)
I would be very grateful if you could help me