plotfun: Plot of Cq distribution

In edpcr: Performs Extended Digital PCR Analysis

Description

Produces plot of the Cq distribution given the provided parameters. Can include a line representing the proprtion of negative partitions.

Usage

plotfun(pars = NULL, h = 0.1, xlim = NULL, 
  dxlim = c(-3, 2.5), new = TRUE, npoints = 10^3, 
  c0 = 6, maxn0 = 7, inc0 = TRUE, type = 0, 
  xlab = expression("C"["q"]), ylab = "density", 
  col = "black", ...)

Arguments

pars	parameters or list, such as cqres object produced by cqmc, that includes the parameters (see type).
h	threshold value
xlim	x-axis range
dxlim	x-axis range relative to approximate mean Cq for 1 initial molecule (used if xlim is NULL).
new	logical, if FALSE, adds plot to existing plot
npoints	number of points calculated for plotting
c0	c0 number of cycles for which exact probabilities are caclulated. This can have a significant impact on speed of computation.
maxn0	the maximum number of initial molecules used in computation.
inc0	logical, if TRUE include line representing fraction of negative partitions.
type	character specifying which vector of parameters to use if pars is a list ("i": pars0, "m": pars.mod, "p": pars.mc).
xlab	x-axis label
ylab	y-axis lable
col	colour of lines
...	plotting parameters

Details

Plots the density of Cq given the specified parameters. The parameters are given by pars and if pars is a list also by type.

If the parameters include "trendx" and/or "trendy" they are ignored.

Value

A list with components:

x	x values plotted.
y	y values plotted.
p0	probability of 0 molecules if inc0 is TRUE and NA otherwise.

Author(s)

Philip Wilson

See Also

plotall

Examples

pars0<-get.pars0(fetch(Exp37a,1))
plotfun(pars0)

# Plot Cq density for posterior mean parameters 
# using result of cqmc.
cqresult<-cqmc(fetch(Exp37a,1),E.init=.9,E1.init=.5,mc.rep=0,mod.rep=200)
plotfun(cqresult,type="m",dxlim=c(-4,3))

edpcr documentation built on May 2, 2019, 5:22 p.m.