knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
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.
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