plotCurve.comb: plot curve from combined fitting

In mengchen18/proturn: System-wise protein turnover curve fitting

Description

plot curve from combined fitting

Usage

plotCurve.comb(x, t, leg.vec = NULL, curve = NULL, tcc = Inf,
  add = FALSE, pch = 20, lty = 1, legend = TRUE, err = TRUE,
  main = "", leg.cex = 1)

Arguments

x	- an element of list returned by fitDegNLS or fitSynNLS
t	time points (hours)
leg.vec	a character vector for legend, the name of the vector should be the same as in x
curve	which curve want to draw. If it's not NULL, should be either "degradation" or "synthesis"
tcc	doubling time of cell lines
add	if the plot should be added on top of another plot
pch	passed to plot
lty	passed to line
legend	logical value, whether legend should be generated
err	a logical value, whether error bar should be plotted
main	the main title of plot
leg.cex	the cex of points in legend

Value

no value to be returned

Examples

# see \code{fitSynNLS}, \code{fitDegNLS}, \code{fitNLSModels}
# simulating data
tp <- c(0, 1, 2, 4, 8, 16, 32, 64)
ratios <- degCurve(A=0.85, B = 0.1, kd=0.5, tcc=Inf, t = tp) + rnorm(length(tp), sd = 0.05)

#' vector input
r <- fitDegNLS(ratios, t = tp, tcc = Inf)
plotCurve(ratios, tp, tcc = Inf, A = r[["A"]], B = r[["B"]], k = r[["kd"]],
          add = FALSE, curve = "deg", err.x = log(2)/r[c("ci025", "ci975")],
          err.y = degCurve(A = r[["A"]], B = r[["B"]], kd = r[["kd"]], t = log(2)/ r[["kd"]], tcc = Inf))

#' matrix input, fit a single model
ratio2 <- rbind(p1 = ratios + rnorm(length(ratios), sd = 0.4),
                p2 = ratios + rnorm(length(ratios), sd = 0.4))
r.mat <- fitDegNLS(ratio2, t = tp, tcc = Inf)
plotCurve(x = ratio2, t = rep(tp, nrow(ratio2)),
          tcc = Inf, A = r.mat[["A"]], B = r.mat[["B"]], k = r.mat[["kd"]],
          add = FALSE, curve = "deg", err.x = log(2)/r.mat[c("ci025", "ci975")],
          err.y = degCurve(A = r.mat[["A"]], B = r.mat[["B"]], kd = r.mat[["kd"]],
                           t = log(2)/ r.mat[["kd"]], tcc = Inf))

#' matrix input, fit a single model, in addition, each individual row should also be fitted
r.mat.ind <- fitDegNLS(ratio2, t = tp, tcc = Inf, fitIndividual = TRUE)
plotCurve.comb(x = r.mat.ind, t = tp, tcc = Inf,
               leg.vec = c(p1="peptide 1", p2 = "peptide 2"), curve = "deg")

mengchen18/proturn documentation built on May 30, 2019, 4:37 p.m.