visualization_deps_with_scatter: Visualize differentially expressed results with scatter

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

Visualize differentially expressed results with scatter

Description

Visualize differentially expressed results with scatter

Usage

visualization_deps_with_scatter(
  deps_data,
  minFC = 2,
  minPvalue = 0.05,
  main = "Differentially expressed proteins",
  show_text = FALSE,
  min_up_text = 15,
  min_down_text = 15
)

Arguments

deps_data	a data frame containing ID, logFC and pvalue.
minFC	a numeric for the minimum fold change.
minPvalue	a numeric for the significance cutoff.
main	an overall title for the plot.
show_text	a boolean value representing whether or not the text is showed, the default is FALSE.
min_up_text	cutoff value for showing up-IDs. Only IDs with lower than min_up_text are showed.
min_down_text	cutoff value for showing down-IDs. Only IDs with lower than min_down_text are showed.

Value

A scatter plot for showing differentially expressed results.

Author(s)

Dongdong Zhan and Mengsha Tong

Examples

## Not run: 
ftp_url <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/visualization_deps_with_scatter.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "visualization_deps_with_scatter.RData")
load("visualization_deps_with_scatter.RData")

visualization_deps_with_scatter(limma_results_df, minFC = 2,
  minPvalue = 0.05, main = 'Differentially expressed proteins  \n with limma',
  show_text = TRUE, min_up_text = 70, min_down_text = 70
)

## End(Not run)

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