# hybridogram

This package takes a list of hybridization experiment results in a simple text file:

species 1 | species 2 | code
--- | --- | ---
Phoca largha | Phoca vitulina | 1
Phoca largha | Phoca caspica | 2
Phoca caspica | Pusa hispida | 2

Another text file contains code for the different hybridization result types:

code | description
--- | ---
1 | No hybrid
2 | Documented hybrid
3 | Hybrid with same 3rd species

Call the hybridogram function:

    library(hybridogram)

    V1 <- c("Phoca largha","Phoca largha","Phoca caspica")
    V2 <- c("Phoca vitulina","Phoca caspica","Pusa hispida")
    V3 <- c(2,3,3)
    hybrid_data <- data.frame(V1,V2,V3)
    C1 <- c(1,2,3)
    C2 <- c("No hybrid","Documented hybrid","Hybrid with same 3rd species")
    codes <- data.frame(C1,C2)
    hybridogram(hybrid_data, codes)

This will produce a heat map, which is the hybridogram. It is a square and symmetric heat map showing the hybrid relationships between all pairs of species. A color legend in the lower right corner shows what color each code is represented by.