env.plot | R Documentation |
Plots the Z statistics at each position within the environment for the requested amino acid.
env.plot(Z, aa, pValue = 0.001, ylim = c(-8,6), ty = 'p',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. |
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. |
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)
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