README.md

In friend1ws/ggseqlogo: A lightweight package for generating sequence logos based on ggplot

ggseqlogo

The R package ggseqlogo is developed for efficiently generating sequence logo figures based on ggplot2, so that the functions provided by ggplot2 and third-party packages for ggplot2 can be effectively used.

• Functions for generating A, C, G, T character polygons are largely extracted from seqLogo package.

Usage

Install the package

First, install devtools for installation of ggseqlogo. ALso, install ggplot2 in case you haven't installed that yet.

install.packages("devtools")
install.packages("ggplot2")

Currently, the only way for installing ggseqlogo is to use devtools:

library(devtools)
devtools::install_github("friend1ws/ggseqlogo")
library(ggseqlogo)

Example

You only need to prepare a DNA frequency matrix (4 * sequence size). The four rows are frequencies of A, C, G, and T nucleotides, respectively. Then, you are all set! You can play with ggplot functions and themes. Also, you can change the colors of A, C, G and T.

M <- matrix(rgamma(20, 1, 10), 4, 5)
ggseqlogo(M)
ggseqlogo(M, is.scale = TRUE) + theme_bw()
ggseqlogo(M, is.scale = TRUE) + theme_classic() + labs(x = "Sequence Num", y = "Prob.")
ggseqlogo(M, is.scale = TRUE, A_col = "green", C_col = "blue", G_col = "orange", T_col = "red") + theme_minimal()

friend1ws/ggseqlogo documentation built on July 28, 2023, 7:17 a.m.