Plot the LOGICOIL scores

Description

This function can be used to plot the results of applying the LOGICOIL prediction algorithm to user-defined coiled-coil sequences. The plot helps visualize the LOGICOIL scores at each position of the coiled-coil sequence.

Usage

plot_LOGICOIL(prob.oligo, id)

Arguments

Details

The required input for this function can be obtained by running the EstimateProbability function (see example).

Value

A PNG file that shows the LOGICOIL prediction scores at each of the position of the input coiled-coil sequence.

Author(s)

Thomas L. Vincent tlfvincent@gmail.com

References

Thomas L. Vincent, Peter J. Green and Dek N. Woolfson. "LOGICOIL-multi-state prediction of coiled-coil oligomeric state", 29(1), pp69-76, Bioinformatics, (2013).

Examples

library(nnet)
data(pssm)
data(Model_Parameters)
data(LOGICOILfit)

cat("Estimating oligomeric state of coiled-coil sequences\n")
prob.oligo <- EstimateProbability("GCN4wt",
  "MKQLEDKVEELLSKNYHLENEVARLKKLV",
  "abcdefgabcdefgabcdefgabcdefga",
  pssm,
  LOGICOILfit,
  Model_Parameters)

# plot LOGICOIL results obtained from user-defined coiled-coil sequences
plot_LOGICOIL(prob.oligo, "GCN4wt")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LOGICOIL)
Loading required package: nnet
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LOGICOIL/plot_LOGICOIL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_LOGICOIL
> ### Title: Plot the LOGICOIL scores
> ### Aliases: plot_LOGICOIL
> 
> ### ** Examples
> 
> library(nnet)
> data(pssm)
> data(Model_Parameters)
> data(LOGICOILfit)
> 
> cat("Estimating oligomeric state of coiled-coil sequences\n")
Estimating oligomeric state of coiled-coil sequences
> prob.oligo <- EstimateProbability("GCN4wt",
+   "MKQLEDKVEELLSKNYHLENEVARLKKLV",
+   "abcdefgabcdefgabcdefgabcdefga",
+   pssm,
+   LOGICOILfit,
+   Model_Parameters)
> 
> # plot LOGICOIL results obtained from user-defined coiled-coil sequences
> plot_LOGICOIL(prob.oligo, "GCN4wt")
png 
  2 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>