plotEmpSplines: Plot the fitted empirical spline of detected proportions to...

In Mengbo-Li/protDP: Estimation of the Detection Probability Curve in Label Free Shotgun Proteomics Data

Plot the fitted empirical spline of detected proportions to average observed intensities

Description

Plot the fitted empirical spline of detected proportions to average observed intensities

Usage

plotEmpSplines(
  nuis,
  X,
  params,
  capped = FALSE,
  add.jitter = TRUE,
  jitter.amount = NULL,
  point.cex = 0.2,
  newPlot = TRUE,
  logit = FALSE,
  lty = "solid",
  lineCol = "darkgreen",
  lwd = 2,
  xlim = NULL,
  ylim = c(0, 1)
)

Arguments

nuis	The list of nuisance parameters.
X	The basis matrix for the natural cubic spline.
params	Fitted coefficients.
capped	Logical. Whether the probabilities are capped by alpha.
add.jitter	Logical. Whether to add jitter to the detected proportion axis.
jitter.amount	Amount of jittering.
point.cex	Size of the points.
newPlot	Logical. Whether to start a new plot device.
logit	Logical. Whether to plot at the logit scale.
lty	Line type.
lineCol	Line color.
lwd	Line width.
xlim	Limits of the x-axis.
ylim	Limits of the y-axis.

Examples

# See the vignettes.

Mengbo-Li/protDP documentation built on Oct. 26, 2023, 9:50 p.m.