plotenz: Plotting the simulated RFLP or TRFLP pattern

In seqRFLP: Simulation and visualization of restriction enzyme cutting pattern from DNA sequences.

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".

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".

Value

Returns the plot of simulated RFLP or TRFLP.

Author(s)

Qiong Ding [e-mail]

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")
		
		

seqRFLP documentation built on May 2, 2019, 6:02 a.m.