Hi,
I just noticed that my command geom_range("height_0.95_HPD", color='gray', size=2, alpha=.5) is putting the bar range centralized in the node heigh, showing equal range in both sides. This is not the expected behavior since the node heights of my MCC tree are not the mean of the tree distribution, but their represent a single tree (the MCC tree).
Below are two images comparing node bars (please ignore the colors) of ggtree
and figtree
and here is my code:
t = ggtree(MCCtree,size=0.5, alpha = 0.8, aes(color=loc),
mrsd="2024-05-23",as.Date = F,
ladderize = T, right = F)
t = t + geom_tippoint(aes(color=loc), size=1, alpha=1) #Colore os tippoints
t = t + geom_nodepoint(aes(subset=(posterior>=0.9), x=branch),size=0.5, color="black", alpha=1) #Node points posterior
t = t + geom_range("height_0.95_HPD", color='gray', size=2, alpha=.5)
t = t + scale_color_manual(values = Locations.col)
t = t + coord_cartesian(clip = "off") + theme_tree2(axis.text.x = element_text(angle=90))#plot.margin = margin(5,10,0,0))
t
Am I doing something wrong or is this a bad behavior of the function?