plotOverall: Plot the conservity of the positions

In hezijin/conservedPos: Use conservedPos find important conserved sites for small target region

Description

This function plots the overall alignment's conservity using the conservity vector generated from the function conservityTable.

Usage

plotOverall(conserV)

Arguments

conserV

a vector with serveral number of conservity

Value

a plot to view the overall alignment's conservity

References

R - Bar Charts: Bar:Chart Labels, Title and Colors. Tutorialpoints-R Tutorial Link

Silva, A. (2020) TestingPackage: An Example R Package For BCB410H. Unpublished. Link

R Bar Plot (2018) DataMentor Getting Started in Data Science With R Link

Examples

# Example 1: Plot a conservity against of each position for testSeqShort

data(testSeqShort)
testSeq <- testSeqShort

# Use conservityTable() to create table for testSeqShort,
# and pass it to plotOverall() for plotting
table  <- conservityTable(testSeq)
oPar <- par(mar = c(2, 4, 2, 1)) # Set plot parameters to layout plot in center.
plotOverall(table)

# Example 2: Plot a conservity against of each position for raw data
# sampleSeq3.txt. This should takes longer time to run.
findpath <- system.file("extdata", "sampleSeq3.txt", package = "conservedPos")
rawSeq <- Biostrings::readBStringSet(findpath,"fasta")

# Use conservityTable() to create table for rawSeq,
# and pass it to plotOverall() for plotting
table <- conservityTable(rawSeq)
oPar <- par(mar = c(2, 4, 2, 1)) # Set plot parameters to layout plot in center.
plotOverall(table)

hezijin/conservedPos documentation built on Jan. 1, 2021, 3:18 a.m.