visualization_fuzzycluster: Visualize results from fuzzy clusters with line chart

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

Visualize results from fuzzy clusters with line chart

Description

Visualize results from fuzzy clusters with line chart

Usage

visualization_fuzzycluster(
  input_data,
  group,
  group_levels,
  k_cluster,
  iteration = 100,
  mfrow = c(3, 3),
  min_mem = 0.1,
  plot = TRUE
)

Arguments

input_data	a data frame containing ID and expression profile.
group	a factor for representing groups.
group_levels	a factor levels for group.
k_cluster	number of clusters fuzzy cluster.
iteration	a numeric value for interation, the defualt is 100.
mfrow	a vector containing 2 elements for controling the subplots in graphic window, the default is mfrow = c(3,3)
min_mem	cutoff value for membership. Only results with greater than min_mem are showed.
plot	a boolean value for deciding whether ploting, the default is TRUE.

Value

A lines chart with fuzzy degree.

Author(s)

Dongdong Zhan and Mengsha Tong

References

(1) David Meyer, Evgenia Dimitriadou, Kurt Hornik, Andreas Weingessel and Friedrich Leisch (2017). e1071: Misc Functions of the \ Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien. R package version 1.6-8.https://CRAN.R-project.org/package=e1071 \ (2) Pengyi Yang (2018). ClueR: Cluster Evaluation. R package version 1.4. https://CRAN.R-project.org/package=ClueR

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_fuzzycluster.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "visualization_fuzzycluster.RData")
load("visualization_fuzzycluster.RData")

fuzzy_clustObj <- visualization_fuzzycluster(
  fuzzy_input_df, group, group_levels,
  k_cluster=9, iteration = 100,
  mfrow = c(3,3), min_mem = 0.1
 )

}

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