In PaolaCognigni/CTraxHelper: CTrax Helper

knitr::opts_chunk$set(echo = FALSE)
require(CTraxHelper)
require(ggplot2)

garn<-readRDS('garn.RDS')

Preferences are calculated based on the position of flies in the last 5 s of each 30-s repeat of the quadrant paradigm. Preference is scored as 1 for each frame inside the lit quadrant and 0 for each frame outside.

PIbyfly<-list()
PIbyrep<-list()
nflies<-length(garn)
flynames<-names(garn)

for (i in 1:nflies) {
  PIbyfly[[i]]<-PIquadrant(garn[[i]]$trx,by.fly=T)
  PIbyrep[[i]]<-PIquadrant(garn[[i]]$trx,by.fly=F) }

PIfly<-data.frame()
PIrep<-data.frame()
for (i in 1:nflies) {
  PIflytemp<-PIbyfly[[i]]
  PIflytemp$id<-factor(PIflytemp$id)
  PIfly<-rbind(PIfly,cbind(PIflytemp,'gen'=flynames[i]))
  PIrep<-rbind(PIrep,cbind(PIbyrep[[i]],'gen'=flynames[i])) 
}

names(PIbyfly)<-flynames
names(PIbyrep)<-flynames

colSums(table(PIfly[,c("id","gen")]))

PIfly<-merge(PIfly,aggregate(PIfly$PI,by=list(gen=PIfly$gen),FUN="mean"))
PIrep<-merge(PIrep,aggregate(PIrep$PI,by=list(gen=PIrep$gen),FUN="mean"))

ggplot(PIrep,aes(x=gen,y=PI)) +
  geom_boxplot(outlier.colour = NA, aes(fill=x)) +
  geom_point(aes(fill=PI), shape=21) +
  scale_fill_gradient2(low="#3A89C9",mid='#FFFAD2',high='#D24D3E', name="PI") +
  ggtitle("PI by repeat") + ylab(NULL) + xlab("genotype")

ggplot(PIfly[!is.na(PIfly$id),],aes(x=gen,y=PI)) +
  geom_boxplot(outlier.colour = NA, aes(fill=x)) +
  geom_point(aes(fill=PI),shape=21) +
  scale_fill_gradient2(low="#3A89C9",mid='#FFFAD2',high='#D24D3E', name="PI") +
  ggtitle("PI by fly") + ylab(NULL) + xlab("genotype")

The PI lists (by fly and by repeat) are saved in r paste(getwd(),"PIbyfly.RDS",sep="/") and r paste(getwd(),"PIbyrep.RDS",sep="/").

saveRDS(PIbyfly,file="PIbyfly.RDS")
saveRDS(PIbyrep,fil="PIbyrep.RDS")

PaolaCognigni/CTraxHelper documentation built on May 7, 2019, 11:57 p.m.