seqRFLP (version 1.0.1)

plotenz: Plotting the simulated RFLP or TRFLP pattern

Description

Plotting the simulated RFLP or TRFLP pattern using selected restriction enzymes.

Usage

plotenz(sequences, enznames, enzdata, side = TRUE, type = c("RFLP", "TRFLP"), Terminal = c("T5", "T3"))

Arguments

sequences

The input data in class fasta containing the DNA sequences.

enznames

The speciefied restriction enzyme names to be applied in RFLP or TRFLP analysis.

enzdata

The dataframe contained enzyme data.

side

Whether to plot the markers for each sequence. Default is TURE which means to plot the marker only once.

type

Pattern type to be specified, should be either "RFLP" or "TRFLP".

Terminal

Terminal noted in "TRFLP" analysis, should be either "T3" or "T5".

Value

Returns the plot of simulated RFLP or TRFLP.

Details

If type = "TRFLP" (The "TRFLP" were selected), the Terminal must also been provided by the user, it's value is either "T3" or "T5".

References

None.

See Also

See Also frag.dat for the summary of RFLP results.

Examples

## plotenz() example

data(enzdata)
data(fil.phy)
fas <- ConvFas(fil = fil.phy, type = "phy")

enznames <- c("EcoRI", "Acc65I", "HinfI")

plotenz(sequences = fas, enznames = enznames, 
        enzdata = enzdata, side = TRUE, type = "RFLP")
		
plotenz(sequences = fas, enznames = enznames, 
        enzdata = enzdata, side = FALSE, type = "RFLP")		
				
plotenz(sequences = fas, enznames = enznames, 
        enzdata = enzdata, side = TRUE, type = "TRFLP", "T3")