Seqlogo

Authors

[Editor] Hu Zheng;

[Contributors]

The sequence LOGO is a graphic that describes a sequence pattern of binding sites.

Setup

System Requirements: Cross-platform (Linux/MacOS/Windows)
Programming language: R
Dependent packages: ggseqlogo; ggplot2

# Install packages
if (!requireNamespace("ggseqlogo", quietly = TRUE)) {
  install.packages("ggseqlogo")
}
if (!requireNamespace("ggplot2", quietly = TRUE)) {
  install.packages("ggplot2")
}

# Load packages
library(ggseqlogo)
library(ggplot2)

Data Preparation

The loaded data is the Sequence of binding sites for multiple transcription factors on multiple genes.

# Load data
data <- read.delim("files/Hiplot/074-ggseqlogo-data.txt", header = T)

# Convert data structure
data <- data[, !sapply(data, function(x) {all(is.na(x))})]
data <- as.list(data)
data <- lapply(data, function(x) {return(x[!is.na(x)])})

# View data
str(data)

List of 12
 $ MA0001.1: chr [1:97] "CCATATATAG" "CCATATATAG" "CCATAAATAG" "CCATAAATAG" ...
 $ MA0002.1: chr [1:26] "AATTGTGGTTA" "ATCTGTGGTTA" "AATTGTGGTAA" "TTCTGCGGTTA" ...
 $ MA0004.1: chr [1:20] "CACGTG" "CACGTG" "CACGTG" "CACGTG" ...
 $ MA0005.1: chr [1:90] "CCTAATTGGGC" "CCTAATTTGGC" "CCTAATCGGGC" "CCTAATCGGGC" ...
 $ MA0006.1: chr [1:24] "CGCGTG" "CGCGTG" "CGCGTG" "CGCGTG" ...
 $ MA0007.1: chr [1:24] "AAAAGTACACCCTGTACCGACA" "CTAAGCACACCGTGTCCCAGTC" "TTAAGAACACTCTGTACGACAC" "AGTAGAACATAATGTTCCGACA" ...
 $ MA0008.1: chr [1:25] "CAATTATT" "CAATTATT" "CAATTATT" "CAATTATT" ...
 $ MA0009.1: chr [1:40] "CTAGGTGTGAA" "CTAGGTGTGAA" "CTAGGTGTGAA" "CTAGGTGTGAA" ...
 $ MA0010.1: chr [1:9] "CTAATTGGCAAATG" "ATAATAAACAAAAC" "GACATAGACAAGAC" "GTCTTTCACAAATA" ...
 $ MA0011.1: chr [1:12] "AACTATTT" "TGCTAGTT" "TCCTAGTT" "TTCTATTC" ...
 $ MA0012.1: chr [1:12] "TAAACTTGTTG" "TAAACTAAAGC" "TCAACTAGGAT" "TAAACAAAACC" ...
 $ MA0013.1: chr [1:6] "TTGTGAAAGAC" "AAGTAAACTAA" "TAATAAACAAA" "TAATAAACAAA" ...

Visualization

# Seqlogo
p <- ggseqlogo(
  data,
  ncol = 4,
  col_scheme = "nucleotide",
  seq_type = "dna",
  method = "bits") + 
  theme(plot.title = element_text(hjust = 0.5))

p

A sequence of binding sites was displayed in a column of the chart by means of BITS calculation, which could clearly observe the large proportion of bases of different sequences.