Why genetic dist. heatmap is all over the plot although I want the lower part?
0
0
Entering edit mode
7 weeks ago
Armin • 0

Hi everyone

I'm trying to generate a heatmap of fst genetic distance, it used to work perfectly, but now the values are all over when I ask for only the lower part. This is the code I'm using:

jm_fst = genet.dist(juglan_sub, method = "WC84") %>% round(digits = 3)

lab_order = c("GAZ", "UAI", "SEM", "KAR", "AZA", "ZAN", "TOY", "KOR", 
              "TAB", "DAM", "IPA", "ARD", "GON", "TAF", "ISF",
              "GEO", "TAL", "QAZ", "QUC", "EGH", "NAG", "URM", "PAV","DEN", "IRA", "BAM", "NUR")

fst.mat = as.matrix(juglan_fst)
fst.mat1 = fst.mat[lab_order, ]
fst.mat2 = fst.mat1[, lab_order]
fst.df$Site1 = factor(fst.df$Site1, levels = unique(fst.df$Site1))
fst.df$Site2 = factor(fst.df$Site2, levels = unique(fst.df$Site2))
ind = which(upper.tri(fst.mat2), arr.ind = TRUE)
fst.df = data.frame(Site1 = dimnames(fst.mat2)[[2]][ind[,2]],
                    Site2 = dimnames(fst.mat2)[[1]][ind[,1]],
                    Fst = fst.mat2[ ind ])


fst.df %>% str
mid = max(fst.df$Fst) / 2

ggplot(data = fst.df, aes(x = Site1, y = Site2, fill = Fst))+
  geom_tile(colour = "black")+
  geom_text(aes(label = Fst), color="black", size = 3)+
  scale_fill_gradient2(low = "blue", mid = "pink", high = "red", midpoint = mid, name = fst.label, limits = c(0, max(fst.df$Fst)), breaks = c(0, 0.05, 0.10, 0.15))+
  scale_x_discrete(expand = c(0,0))+
  scale_y_discrete(expand = c(0,0), position = "right")+
  theme(axis.text = element_text(colour = "black", size = 10, face = "bold"),
        axis.title = element_blank(),
        panel.grid = element_blank(),
        panel.background = element_blank(),
        legend.position = "right",
        legend.title = element_text(size = 14, face = "bold"),
        legend.text = element_text(size = 10)
  )

This is the plot but it supposed to be a triangle

distance Heatmap ggplot genetic • 174 views
ADD COMMENT

Login before adding your answer.

Traffic: 1495 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6