#------------------- #------------------- # Visualizing Parentage Analysis #------------------- setwd("/users/mariestrader/Documents/ColorMorphGE/ProcB/Dryad") library(ggplot2) par=read.csv("ParentsRJune2015.csv") head(par) par$number=as.factor(par$number) par$parent1=as.factor(par$parent1) par$parent2=as.factor(par$parent2) par$parentA=as.factor(par$parentA) par$parentB=as.factor(par$parentB) par$parents=as.factor(par$parents) summary(par) #-------------Describing the parents of different color morphs green=subset(par, color=="green") mega=subset(par, color=="Mega") red=subset(par, color=="red") length(green[,1]) #34 length(mega[,1]) #18 length(red[,1]) #10 summary(green$parents) #12 1A 1B 2A 2B AB # 5 1 4 0 21 3 summary(red$parents) #12 1A 1B 2A 2B AB # 5 1 0 4 0 0 summary(mega$parents) #12 1A 1B 2A 2B AB # 8 0 2 6 1 1 P12=subset(par, parents=="12") P1A=subset(par, parents=="1A") P1B=subset(par, parents=="1B") P2A=subset(par, parents=="2A") P2B=subset(par, parents=="2B") PAB=subset(par, parents=="AB") length(P12[,1]) #18 length(P1A[,1]) #2 length(P1B[,1]) #6 length(P2A[,1]) #10 length(P2B[,1]) #22 length(PAB[,1]) #4 summary(P12$color) #green Mega red # 5 8 5 summary(P1A$color) #green Mega red # 1 0 1 summary(P1B$color) #green Mega red # 4 2 0 summary(P2A$color) #green Mega red # 0 6 4 summary(P2B$color) #green Mega red # 21 1 0 summary(PAB$color) #green Mega red # 3 1 0 #-------------Stacked bar plot par=read.csv("props_stacked.csv") summary(par) qplot(factor(parent), y= prop_parent, data=par, geom="bar", fill=factor(color), stat="identity")