##to turn original responsive/not responsive data into proportions: Fig6all <- read.csv(file.choose(), header=T) ##Figure 6a: WTtapsresponsiveindiv <- data.frame(aggregate(responsiveindiv ~ Dose+tap.number, WTFig6all, sum)) WTtapsresponsiveindiv$Dose <- as.factor(WTtapsresponsiveindiv$Dose) WTtapsresponsiveindiv$tap.number.Dose <- paste(WTtapsresponsiveindiv$tap.number,WTtapsresponsiveindiv$Dose) WTFig6all$tap.number.Dose <- paste(WTFig6all$tap.number, WTFig6all$Dose) WTtapsresponsiveindiv$total.individuals <- table(WTFig6all$tap.number.Dose) WTtapsresponsiveindiv$prop <- (WTtapsresponsiveindiv$responsiveindiv/WTtapsresponsiveindiv$total.individuals) ggplot(WTtapsresponsiveindivnodrug, aes(x=tap.number, y=prop, group=1))+ geom_point()+ geom_smooth(method=lm,formula= (y ~ log(x)), se=FALSE)+ scale_x_continuous(breaks=c(1,2,3,4,5,6,7,8,9,10))+ theme_bw() + ylim(0,0.8)+ labs(x="stimulus event number", y="proportion of WT individuals responding") + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank()) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank())+ theme(axis.title = element_text(size = 13))+ theme_classic() ##Figure 6c: Genotypes (no drug) nodrugFig6all <- subset(Fig6all, Dose=="0") nodrugtapsresponsiveindiv <- data.frame(aggregate(responsiveindiv ~ Genotype+tap.number, nodrugFig6all, sum)) nodrugtapsresponsiveindiv$tap.number.Genotype <- paste(nodrugtapsresponsiveindiv$tap.number,nodrugtapsresponsiveindiv$Genotype) nodrugFig6all$tap.number.Genotype <- paste(nodrugFig6all$tap.number,nodrugFig6all$Genotype) nodrugtapsresponsiveindiv$total.individuals <- table(nodrugFig6all$tap.number.Genotype) nodrugtapsresponsiveindiv$prop <- (nodrugtapsresponsiveindiv$responsiveindiv/nodrugtapsresponsiveindiv$total.individuals) ggplot(nodrugtapsresponsiveindiv, aes(x=tap.number, y=prop, colour=Genotype))+ geom_point()+ geom_smooth(method=lm,formula= (y ~ log(x)), se=FALSE)+ scale_x_continuous(breaks=c(1,2,3,4,5,6,7,8,9,10))+ theme_bw() + labs(x="stimulus event number", y="proportion of individuals from \n each genotype responding") + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank()) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank())+ ylim(0,0.8)+ theme(axis.title = element_text(size = 13))+ theme_classic() ##Figure 6d (genotype by dose across all taps) notapnumberresponsiveindiv <- data.frame(aggregate(responsiveindiv ~ Genotype+Dose, Fig6all, sum)) notapnumberresponsiveindiv$Dose <- as.factor(notapnumberresponsiveindiv$Dose) notapnumberresponsiveindiv$DoseGenotype <- paste(notapnumberresponsiveindiv$Dose, notapnumberresponsiveindiv$Genotype) notapnumberresponsiveindiv$total.individuals <- table(Fig6all$DoseGenotype) notapnumberresponsiveindiv$prop <- (notapnumberresponsiveindiv$responsiveindiv/notapnumberresponsiveindiv$total.individuals) notapnumberresponsiveindiv$Dose.num <- as.numeric(notapnumberresponsiveindiv$Dose) notapnumberresponsiveindiv$prop <- as.numeric(notapnumberresponsiveindiv$prop) ggplot(notapnumberresponsiveindiv, aes(x=Dose.num, y=prop, colour=Genotype,))+ geom_point()+ geom_line(aes(color=Genotype))+ theme_bw() + labs(x="Dose (mg/L", y="proportion of individuals from each \n genotype responding to stimulus") + scale_x_continuous(breaks=c(1,2,3,4),labels=c("0.0", "0.05", "0.10", "0.50"))+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank()) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank())+ theme(plot.title = element_text(hjust = 0.5))+ theme_classic() ##Figure 6e WTFig6all <- subset(Fig6all, Genotype=="WT") WTbydoseresponsiveindiv <- data.frame(aggregate(responsiveindiv ~ tap.number+Dose, WTFig6all, sum)) WTbydoseresponsiveindiv$Dose <- as.factor(WTbydoseresponsiveindiv$Dose) WTbydoseresponsiveindiv$tap.number.Dose <- paste(WTbydoseresponsiveindiv$Dose, WTbydoseresponsiveindiv$tap.number) WTFig6all$tap.number.Dose <- paste(WTFig6all$Dose, WTFig6all$tap.number) WTbydoseresponsiveindiv$total.individuals <- table(WTFig6all$tap.number.Dose) WTbydoseresponsiveindiv$prop <- (WTbydoseresponsiveindiv$responsiveindiv/WTbydoseresponsiveindiv$total.individuals) ggplot(WTbydoseresponsiveindiv, aes(x=tap.number, y=prop, colour=Dose,))+ geom_point()+ theme_bw() + geom_smooth(aes(color=Dose),method=lm,formula= (y ~ log(x)), se=FALSE)+ labs(x="stimulus event number", y="proportion of WT individuals from each \n dose responding to stimulus") + scale_x_continuous(breaks=c(1,2,3,4,5,6,7,8,9,10))+ scale_color_discrete(name = "Dose (mg/L)", labels = c("0.0", "0.05", "0.10", "0.5"))+ ylim(0,0.8)+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank()) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank())+ theme(axis.title = element_text(size = 13))+ theme_classic() ##Figure 6f HOMFig6all <- subset(Fig6all, Genotype=="HOM") HOMbydoseresponsiveindiv <- data.frame(aggregate(responsiveindiv ~ tap.number+Dose, HOMFig6all, sum)) HOMbydoseresponsiveindiv$Dose <- as.factor(HOMbydoseresponsiveindiv$Dose) HOMbydoseresponsiveindiv$tap.number.Dose <- paste(HOMbydoseresponsiveindiv$Dose, HOMbydoseresponsiveindiv$tap.number) HOMFig6all$tap.number.Dose <- paste(HOMFig6all$Dose, HOMFig6all$tap.number) HOMbydoseresponsiveindiv$total.individuals <- table(HOMFig6all$tap.number.Dose) HOMbydoseresponsiveindiv$prop <- (HOMbydoseresponsiveindiv$responsiveindiv/HOMbydoseresponsiveindiv$total.individuals) ggplot(HOMbydoseresponsiveindiv, aes(x=tap.number, y=prop, colour=Dose,))+ geom_point()+ geom_smooth(aes(color=Dose), method=lm,formula= (y ~ log(x)), se=FALSE)+ theme_bw() + labs(x="stimulus event number", y="proportion of HOM individuals from each \n dose responding to stimulus") + scale_x_continuous(breaks=c(1,2,3,4,5,6,7,8,9,10))+ scale_color_discrete(name = "Dose (mg/L)", labels = c("0.0", "0.05", "0.10", "0.50"))+ ylim(0,0.8)+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank()) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank())+ theme(axis.title = element_text(size = 13))+ theme_classic()