plotPi0: Confidence intervals for pi[0]

In epurdom/cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

Description

A plotting function to plot the confidence intervals of the estimated pi[0] values returned from eventTiming

Usage

plotPi0(est, ui, li, samples, labels = NULL, xlab = "Segment", 
	ylab = expression(pi[0]), 
	pchFac = rep(1, length(est)), whHighlight = NULL, 
	nMut = NULL, xorder = NULL, ...)

Arguments

est	vector of the estimates of pi[0]
ui	vector of the upper values for the confidence interval of the pi[0]
li	vector of the lower values for the confidence interval of the pi[0]
samples	vector indicating which sample each pi[0] corresponds to (will be converted to factor with factor command)
labels	character vector of the labels of each estimate (optional)
xlab	label for the xaxis, defaults to “Segment”
ylab	label for the yaxis, defaults to “pi[0]”
pchFac	vector of pch values for the center of the confidence interval
whHighlight	a vector of indices of the estimates that should be ‘highlighted’ by coloring their confidence intervals red (optional)
nMut	a vector of values of the number of mutations from each confidence interval to be printed at the top of the plot
xorder	a vector giving an ordering of the estimates for the confidence intervals; if NULL, an order within each sample is created automatically.
...	arguments passed to plotCI function

Value

The order of the estimates found internally by the program (or given by the user) are returned invisibly.

Author(s)

Elizabeth Purdom

See Also

plotCI, eventTiming

epurdom/cancerTiming documentation built on May 16, 2019, 8:21 a.m.