plotPartial: This function plots the conservity for selected alignment...

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

Description

This function plots the conservity for selected alignment region from user using the conservity vector.

Usage

plotPartial(conserV, firstIndex, lastIndex)

Arguments

conserV	a vector with serveral number of conservity
firstIndex	a number to point the start index of selected region
lastIndex	a number to point the end index of selected region

Value

a plot to view the seleted region 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 Unpublished.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
# from position 2 to 15
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.
plotPartial(table, 2, 15)

# Example 2: Plot a conservity against of each position for raw data
# from position 50 to 100
# 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(testSeq)
oPar <- par(mar = c(2, 4, 2, 1)) # Set plot parameters to layout plot in center.
plotPartial(table, 50, 100)

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