b2_plotmodel: Plot Fitted Models

In cubfits: Codon Usage Bias Fits

Description

Plot model results to visualize the effects of mutation and selection along with expression levels. The model can be fitted by MCMC or multinomial logistic regression.

Usage

  prop.model.roc(b.Init, phi.Obs.lim = c(0.01, 10), phi.Obs.scale = 1,
                 nclass = 40, x.log10 = TRUE)

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

  plotaddmodel(ret.model, lty, u.codon = NULL, color = NULL,
               x.log10 = TRUE)

Arguments

b.Init	a b object.
phi.Obs.lim	range of phi.Obs.
phi.Obs.scale	optional scaling factor.
nclass	number of binning classes across the range of phi.Obs.
x.log10	log10() transformation of X-axis.
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.
u.codon	unique synonymous codon names.
color	a color vector for unique codon, typically returns of the internal function get.color().
...	options passed to plot().

Details

The function plotmodel() plots the fitted curves obtained from prop.model.roc().

The function plotaddmodel() can append model curves to a binning plot provided unique synonymous codons and colors are given. This function is nearly for an internal call within plotmodel(), but is exported and useful for workflow.

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

Value

A fitted curve plot is drawn.

Author(s)

Wei-Chen Chen [e-mail].

References

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

See Also

plotbin(), prop.bin.roc(), and prop.model.roc().

Examples

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

## End(Not run)

cubfits documentation built on Nov. 8, 2021, 1:07 a.m.