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: data.table; jsonlite; ggseqlogo; ggplot2

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

# Load packages
library(data.table)
library(jsonlite)
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 <- data.table::fread(jsonlite::read_json("https://hiplot.cn/ui/basic/ggseqlogo/data.json")$exampleData$textarea[[1]])
data <- as.data.frame(data)

# 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[1:5])
List of 5
 $ 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" ...

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.