Plotmodel {cubfits}

Plot Fitted Models

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)