alnDotPlot

The goal of alnDotPlot is to generate and plot dot matrices of pairwise sequence alignments.

Installation

You can install the development version of alnDotPlot from GitHub with:

# install.packages("devtools")
devtools::install_github("jgarciamesa/alnDotPlot")

Example

This is a basic example on how to load and plot alignments.

library(alnDotPlot)
# load and plot fasta sample
sample_data = system.file("extdata/samples", "1.fa", package = "alnDotPlot")
plot_dot_matrix(sample_data)

# load and plot json sample using ggplot
sample_data = system.file("extdata", "sample.json", package = "alnDotPlot")
plot_dot_matrix(input = sample_data, use_ggplot = TRUE)

# load and read all fasta samples contained in a folder
sample_data = system.file("extdata/samples", package = "alnDotPlot")
plot_dot_matrix(input = sample_data)