Description Usage Arguments Author(s) See Also Examples
Functions to plot FLIM results.
1 2 3 4 5 6 7 8 | plotHistAmp(multimodel, t, i=1)
plotHistNormComp(multimodel, t, i=1)
plotIntenImage(multimodel, t, i=1, tit=c("Intensity Image"))
plotSelIntenImage(multimodel, t, i=1, tit=c("Region of Interest"),
cex=1)
plotTau(multimodel, t, i=1, tit=" < tau > ", plotoptions=kinopt(),
lifetimes=TRUE)
plotNormComp(multimodel, t, i=1)
|
multimodel |
the |
t |
the |
i |
dataset index to make plot for |
tit |
Character vector giving the title |
plotoptions |
object of class |
cex |
A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default |
lifetimes |
A logical value indicating whether the averages per-pixel should be for lifetimes or their inverse, decay rates. |
Katharine M. Mullen, Sergey Laptenok, Ivo H. M. van Stokkum
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 | ## Not run:
##############################
## READ IN DATA, PREPROCESS DATA
##############################
## data representing only donor tagged
data("donorTagged")
D1 <- preProcess(c001, sel_time=c(25,230))
D2 <- preProcess(c003, sel_time=c(25,230))
## data representing donor-acceptor tagged
data("donorAcceptorTagged")
DA1 <- preProcess(cy005c, sel_time=c(25,230))
DA2 <- preProcess(cy006, sel_time=c(25,230))
##############################
## READ IN MEASURED IRF, PREPROCESS IRF
##############################
data("mea_IRF")
mea_IRF <- baseIRF(mea_IRF, 100, 150)[25:230]
##############################
## SPECIFY INITIAL MODEL
##############################
modelC <- initModel(mod_type = "kin",
## starting values for decays
kinpar=c(1.52, 0.36),
## numerical convolution algorithm to use
convalg = 2,
## measured IRF
measured_irf = mea_IRF,
## shift of the irf is fixed
parmu = list(0), fixed = list(parmu=1),
## one component represents a pulse-following with the IRF shape
cohspec = list(type = "irf"),
## parallel kinetics
seqmod=FALSE,
## decay parameters are non-negative
positivepar=c("kinpar"),
title="Global CFP bi-exp model with pulse-follower")
##############################
## FIT MODEL FOR DONOR ONLY DATA
##############################
fitD <- fitModel(list(D1,D2),
list(modelC),
## estimate the linear coeefficients per-dataset
modeldiffs = list(linkclp=list(1,2)),
opt=kinopt(iter=1, linrange = 10,
addfilename = TRUE,
output = "pdf",
makeps = "globalD",
notraces = TRUE,
selectedtraces = seq(1, length(c001@x2), by=11),
summaryplotcol = 4, summaryplotrow = 4,
ylimspec = c(1, 2.5),
xlab = "time (ns)", ylab = "pixel number",
FLIM=TRUE))
##############################
## FIT MODEL FOR DONOR-ACCEPTOR DATA
##############################
fitDA <- fitModel(list(DA1,DA2),
list(modelC),
## estimate the linear coeefficients per-dataset
modeldiffs = list(linkclp=list(1,2)),
opt=kinopt(iter=1, linrange = 10,
addfilename = TRUE,
output = "pdf",
makeps = "globalDA",
notraces = TRUE,
selectedtraces = seq(1, length(c001@x2), by=11),
summaryplotcol = 4, summaryplotrow = 4,
ylimspec = c(1, 2.5),
xlab = "time (ns)", ylab = "pixel number",
FLIM=TRUE))
##############################
## COMPARE THE DECAY RATES
##############################
parEst(fitD)
parEst(fitDA)
##############################
## ADDITIONAL FIGURES
##############################
par(mfrow=c(2,2), mar=c(1,3,1,12))
par(cex=1.5)
plotIntenImage(fitD$currModel, fitD$currTheta, 1, tit="")
par(cex=1.5)
plotIntenImage(fitDA$currModel, fitD$currTheta, 1, tit="")
par(cex=1.5)
plotIntenImage(fitD$currModel, fitD$currTheta, 2, tit="")
par(cex=1.5)
plotIntenImage(fitDA$currModel, fitD$currTheta, 2, tit="")
###############
plo <- kinopt(ylimspec = c(.25,1.1), imagepal=grey(seq(1,0,length=100)))
par(mfrow=c(2,2), mar=c(1,3,1,12))
par(cex=1.5)
plotTau(fitD$currModel, fitD$currTheta, 1, tit="",plotoptions=plo,
lifetimes=FALSE)
par(cex=1.5)
plotTau(fitDA$currModel, fitD$currTheta, 1, tit="",plotoptions=plo,
lifetimes=FALSE)
par(cex=1.5)
plotTau(fitD$currModel, fitD$currTheta, 2, tit="",plotoptions=plo,
lifetimes=FALSE)
par(cex=1.5)
plotTau(fitDA$currModel, fitD$currTheta, 2, tit="", plotoptions=plo,
lifetimes=FALSE)
## End(Not run)
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