env.plot: Differential Sequence Environment Plot
In jcaledo/ptm_0.1.1: Analyses of Protein Post-Translational Modifications

Description Usage Arguments Details Value Author(s) References See Also Examples

Plots the Z statistics at each position within the environment for the requested amino acid.

1	env.plot(Z, aa, pValue = 0.001, title = "")

`Z`	a matrix containing the standardized difference in frequencies (positive - control).
`aa`	the amino acid of interest.
`pValue`	the p-Value chosen to confer statistical significance.
`title`	character string giving a title for the plot.

The p-Value is used to draw two horizontal lines delimiting the region supporting the null hypothesis: no significant differences. Points laying above or below of these lines cannot be explained by randomness.

This function returns a plot for the requested amino acid.

Juan Carlos Aledo

Aledo et al. Sci Rep. 2015; 5: 16955. (PMID: 26597773)

env.extract(), env.matrices() and env.Ztest()

## Not run: ## Get the matrices
pos = env.matrices(hmeto$positive)[[2]][,-11]
ctr = env.matrices(hmeto$control)[[2]][,-11]
## Run the test
Z = env.Ztest(pos, ctr, alpha = 0.0001)[[1]]
## Plot the results
env.plot(Z, aa = 'E', pValue = 0.05)
## End(Not run)