b1_plotbin: Plot Binning Results

In snoweye/cubfits: Codon Usage Bias Fits

Description

Plot binning results to visualize the effects of mutation and selection along with expression levels empirically.

Usage

  prop.bin.roc(reu13.df, phi.Obs = NULL, nclass = 20, bin.class = NULL,
               weightedCenters = TRUE, logBins = FALSE)

  plotbin(ret.bin, ret.model = NULL, main = NULL,
          xlab = "Production Rate (log10)", ylab = "Proportion",
          xlim = NULL, lty = 1, x.log10 = TRUE, stderr = FALSE, ...)

Arguments

reu13.df	a reu13.df object.
phi.Obs	a phi.Obs object.
nclass	number of binning classes across the range of phi.Obs.
bin.class	binning proportion, e.g. c(0, seq(0.05, 0.95, length = nclass), 1).
ret.bin	binning results from prop.bin.roc().
weightedCenters	if centers are weighted.
logBins	if use log scale for bin.
ret.model	model results from prop.model.roc().
main	an option passed to plot().
xlab	an option passed to plot().
ylab	an option passed to plot().
xlim	range of X-axis.
lty	line type if ret.model is provided.
x.log10	log10() transformation of X-axis.
stderr	plot stand error instead of stand deviation.
...	options passed to plot().

Details

The function plotbin() plots the binning results ret.bin returned from prop.bin.roc(). Fitted curves may be added if ret.model is provided which can be obtained from prop.model.roc().

plotaddmodel() can append model later if ret.model is not provided to plotbin().

Currently, only ROC model is supported. Colors are controlled by .CF.PT.

Value

A binning plot is drawn.

Author(s)

Wei-Chen Chen [e-mail].

References

https://github.com/snoweye/cubfits/

See Also

plotmodel() and prop.model.roc().

Examples

## Not run: 
demo(plotbin, 'cubfits', ask = F, echo = F)

## End(Not run)

snoweye/cubfits documentation built on Nov. 9, 2021, 3:39 a.m.