Nothing
setMethod("show", "Bli", function(object) {
cat(is(object)[[1]], "Class \n==========\n")
cat("status:\n")
print(object@status)
cat("--------------------\ntraces: data.frame with 1st column of time\n")
if (length(object@traces) == 0)
cat("empty\n") else {
print(object@traces[1:min(5, nrow(object@traces)), 1:min(6, ncol(object@traces))])
cat(ncol(object@traces) - 1, "traces,", nrow(object@traces), "time points\n")
}
cat("--------------------\nligand: concentration from high to low\n")
if (length(object@lig) == 0)
cat("empty\n") else print(object@lig)
cat("--------------------\ntExp: start Time of associationa and dissociation\n")
if (length(object@tExp) == 0)
cat("empty\n") else print(object@tExp)
cat("--------------------\nkOn0: initial On-rate ")
if (length(object@kOn0) == 0)
cat("(to be 'estimate'd or input)\n") else cat(object@kOn0, "\n")
cat("--------------------\nkOff0: initial Off-rate ")
if (length(object@kOff0) == 0)
cat("(to be 'estimate'd or input)\n") else cat(object@kOff0, "\n")
cat("--------------------\nkinetics: fitting model\n")
print(summary(object@kinetics))
cat("--------------------\n")
})
setGeneric("plotTraces", function(obj, ...) standardGeneric("plotTraces"))
setMethod("plotTraces", "Bli", function(obj, ...) {
if (!length(obj@traces) > 0)
stop("traces is empty")
t <- obj@traces[, 1]
traces <- obj@traces[, 2:ncol(obj@traces)]
colFun = colorRampPalette(c("cyan", "magenta"))
palet = colFun(ncol(traces))
color = adjustcolor(palet, alpha.f = 0.3)
plot(t, traces[, 1], type = "l", ylim = range(traces), col = color[1], xlab = "Time (s)",
ylab = "Response (nm)", ...)
for (i in 2:ncol(traces)) lines(t, traces[, i], col = color[i], ...)
abline(v = obj@tExp, lty = 2, ...)
})
setGeneric("plotKinetics", function(obj, ...) standardGeneric("plotKinetics"))
setMethod("plotKinetics", "Bli", function(obj, ...) {
if (!length(obj@kinetics) > 1)
stop("not fitting kinetics yet")
t <- obj@traces[, 1]
traces <- obj@traces[, 2:ncol(obj@traces)]
traces <- traces[which(t >= obj@tExp[1]), ]
t <- t[which(t >= obj@tExp[1])] - obj@tExp[1]
yF <- predict(obj@kinetics)
dim(yF) <- dim(traces)
colFun = colorRampPalette(c("cyan", "magenta"))
color1 = colFun(ncol(traces))
color = adjustcolor(color1, alpha.f = 0.3)
plot(t, traces[, 1], type = "l", ylim = range(traces), col = color[1], xlab = "Time (s)",
ylab = "Response (nm)", ...)
for (i in 2:ncol(traces)) lines(t, traces[, i], col = color[i], ...)
for (i in 1:ncol(traces)) lines(t, yF[, i], col = color1[i], ...)
abline(v = diff(obj@tExp), lty = 2, ...)
})
setGeneric("plotResiduals", function(obj, ...) standardGeneric("plotResiduals"))
setMethod("plotResiduals", "Bli", function(obj, ...) {
if (!length(obj@kinetics) > 1)
stop("not fitting kinetics yet")
t <- obj@traces[, 1]
traces <- obj@traces[, 2:ncol(obj@traces)]
traces <- traces[which(t >= obj@tExp[1]), ]
t <- t[which(t >= obj@tExp[1])] - obj@tExp[1]
yF <- predict(obj@kinetics)
dim(yF) <- dim(traces)
yF = traces - yF
colFun = colorRampPalette(c("cyan", "magenta"))
color1 = colFun(ncol(traces))
color = adjustcolor(color1, alpha.f = 0.3)
bound <- diff(range(traces))/2
plot(t, yF[, 1], type = "l", ylim = c(-bound, bound), col = color[1], xlab = "Time (s)",
ylab = "Response (nm)", ...)
for (i in 2:ncol(yF)) lines(t, yF[, i], col = color[i], ...)
abline(v = diff(obj@tExp), lty = 2, ...)
abline(h = 0, ...)
})
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