https://github.com/maartenpaul/DBD_tracking
Revision 36f032f51402940b51db3b5835153ca6552ce15b authored by Maarten Paul on 07 March 2022, 11:26:44 UTC, committed by GitHub on 07 March 2022, 11:26:44 UTC
1 parent 9c823c5
Tip revision: 36f032f51402940b51db3b5835153ca6552ce15b authored by Maarten Paul on 07 March 2022, 11:26:44 UTC
Update README.md
Update README.md
Tip revision: 36f032f
MSD_fit.R
track_msd_fit <- function(x,n=5,fitzero=T,framerate=1/33,pxsize=100,offset=4*0.01^2,dim=2){
#apply function for every track (column V4)
coef <- ddply(x[,-6],.variables = "track", function(x) {
mst <- t(x[,-1])
time <- seq(1,length(mst),1)
time <- time/framerate/1000 #convert frame to second
#plot(mst,ylim=c(0,0.5),xlim=c(0,10))
if(fitzero){
mst <- mst-offset
fit <- tryCatch(lm(formula = mst ~ time-1), error=function(e) NULL)
} else if (fitzero==FALSE) {
fit <- tryCatch(nls(formula = mst[,1] ~ time*x1+x2,lower = list(x1=0,x2=0),start=list(x1=0,x2=0),algorithm = "port"), error=function(e) NULL)
}
if (!is.null(fit)){
RSS.p <- sum(residuals(fit)^2)
TSS <- sum((mst - mean(mst,na.rm = T))^2,na.rm = T)
rsq <- 1-(RSS.p/TSS)
coef <- c(coef(fit)[1],offset,rsq)
coef[1] <- coef[1]/(2*dim)
return(coef)
}
# MSD=4*D*t
})
names(coef) <- c("track","D","intercept","Rsquared")#,paste("dx_",1:n,sep=""),paste("N_",1:n,sep=""))
return (coef)
}
TRACK_MSD_fit <- function(x,n,fitzero,framerate,pxsize,offset,dim){
UseMethod("TRACK_MSD_fit")
}
TRACK_MSD_fit.default <- function(x,n=5,fitzero=T,framerate=1/33,pxsize=100,offset=4*0.01^2,dim=2){
stop("MSD_fit requires data frame")
}
TRACK_MSD_fit.data.frame <- function(x,n=5,fitzero=T,framerate=1/33,pxsize=100,offset=4*0.01^2,dim=2){
track_msd_fit(x,n,fitzero,framerate,pxsize,offset,dim)
}
TRACK_MSD_fit.list <- function(x,n=5,fitzero=T,framerate=1/33,pxsize=100,offset=4*0.01^2,dim=2){
llply(x,.progress = "text",function(x){
out <- TRACK_MSD_fit(x,n,fitzero,framerate,pxsize,offset,dim)
out$cellID <- x$cellID[1]
return(out)
})
}
Computing file changes ...