visualization_with_simple_tsne: A simple t-SNE plot.

In ecnuzdd/PhosMap: A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

A simple t-SNE plot.

Description

A simple t-SNE plot.

Usage

visualization_with_simple_tsne(
  expr_data_frame,
  group,
  main = "Simple t-SNE",
  perplexity = 10
)

Arguments

expr_data_frame	A data frame containing ID and quantification value.
group	A factor for group information.
main	The main title of plot.
perplexity	A numerical value for perplexity, the default is 10.

Value

A simple t-SNE plot.

Author(s)

Dongdong Zhan and Mengsha Tong

Examples

## The process needs to load data from PhosMap datasets stored into FTP server and perform large computation.
## It may take a few minutes.
if(FALSE){
ftp_url <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/visualization_with_simple_tsne.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "visualization_with_simple_tsne.RData")
load("visualization_with_simple_tsne.RData")

visualization_with_simple_tsne(
  expr_data_frame,
  group,
  main = 'Simple t-SNE',
  perplexity = 12
)

}

ecnuzdd/PhosMap documentation built on Dec. 7, 2022, 4:09 a.m.