ptm (version 0.2.2)

env.plot: Differential Sequence Environment Plot

Description

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

Usage

env.plot(Z, aa, pValue = 0.001, ylim = c(-8,6), ty = 'p',title = "")

Arguments

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.

ylim

range of the dependent variable. If we pass the argument 'automatic', the function will choose a suitable range for you.

ty

what type of plot should be drawn ("p": points, "l": lines, "b": both).

title

character string giving a title for the plot.

Value

This function returns a plot for the requested amino acid.

Details

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.

References

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

See Also

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

Examples

# 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)
# }