c0_plot: Cedric Plot Utilities

In cubfits: Codon Usage Bias Fits

Description

This utility function provides basic plots by Cedric.

Usage

  plotPTraces(pMat, ...)
  
  plotExpectedPhiTrace(phiMat, ...)
  
  plotCUB(reu13.df.obs, bMat = NULL, bVec = NULL, phi.bin,
          n.use.samples = 2000, main = "CUB", model.label = c("True Model"),
          model.lty = 1, weightedCenters = TRUE)

  plotTraces(bMat, names.aa, param = c("logmu", "deltaeta", "deltat"),
             main = "AA parameter trace")

Arguments

reu13.df.obs	under development
bVec	a parameter vector
phi.bin	phi values to bin for comparison
n.use.samples	under development
main	Main name for plotTraces
model.label	Name of model
model.lty	line type for model
weightedCenters	if centers are weighted.
names.aa	List of amino acids used for estimation
param	select to plot parameter trace for either log(mu) values or delta t
phiMat	phi matrix from the output of "cubmultichain", "cubsinglechain", "cubfits", "cubappr", or "cubpred"
bMat	b matrix from the output of "cubmultichain", "cubsinglechain", "cubfits", "cubappr", or "cubpred"
pMat	p matrix from the output of "cubmultichain", "cubsinglechain", "cubfits", "cubappr", or "cubpred"
...	other ploting options

Details

under development

Value

under development

Author(s)

Cedric Landerer [e-mail].

References

https://github.com/clandere/cubfits/

See Also

plot

Examples

## Not run: 
suppressMessages(library(cubfits, quietly = TRUE))


## End(Not run)

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