In PaolaCognigni/CTraxHelper: CTrax Helper

verbose=FALSE

datafile<-file.choose()
load(datafile)
proceed=FALSE
if (exists("garn")) {proceed=TRUE}

This report plots the preference behaviours in a quadrant activation paradigm (sections 4 and 5 of the protocol). Data is extracted from the garn list from the data file r paste(dirname(datafile),basename(datafile),sep="/").

r if (proceed) {("PIs are calculated averaging the quadrant (*on* or *off*) in which flies are found for the last 90 frames (5s) of the quadrant protocol. These are averaged by fly (over 4 quadrant repeats; therefore giving roughly N=number of flies, unless tracks have split during the experiment) or by protocol repeat (therefore always giving N=4).")} else {("The plotting cannot proceed as the data file does not contain the appropriate variable.")}

require(CTraxHelper)
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) {
  PIfly<-rbind(PIfly,cbind(PIbyfly[[i]],'gen'=flynames[i]))
  PIrep<-rbind(PIrep,cbind(PIbyrep[[i]],'gen'=flynames[i])) 
}

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"))

require(ggplot2)  

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")