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guokai8 / CandiHap

Build haplotye and generate figures
GNU General Public License v3.0
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Plot Gene LDheatmap #1

Open xukaili opened 4 years ago

xukaili commented 4 years ago

want to extract results (For V0.0.15)

Hap_results <- results(hap, gene="Si9g49990")

Plot Gene LDheatmap

if (! require("LDheatmap")) install.packages("LDheatmap")
if (! require("genetics")) install.packages("genetics")
LDsnp <- Hap_results[, !names(Hap_results) %in% c("sample","Info")]
LDsnp = LDsnp[,-ncol(LDsnp)]
NAs <- LDsnp == "N/N"
is.na(LDsnp)[NAs] <- TRUE
LDsnp[NAs] <- NA
LDsnp = LDsnp[-1,]
Dist = as.numeric(LDsnp[1,])
LDsnp = LDsnp[-c(1:6),]
num<-ncol(LDsnp) 
for(i in 1:num){
    LDsnp[,i]<-as.genotype(LDsnp[,i]) 
}
rgb.palette <- colorRampPalette(rev(c("#1F77B4", "#AEC7E8", "#FF7F0E")), space = "rgb")
LDheatmap(LDsnp, genetic.distances = Dist, flip = TRUE, color=rgb.palette(40))