Plotbin {cubfits}

Plot Binning Results

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)