rhcoclust_internet: Interaction network (internet) of the 'rhcoclust' objects

In mdbahadur/rhcoclust: Robust Hierarchical Co-Clustering to Identify Significant Co-Cluster

Interaction network (internet) of the 'rhcoclust' objects

Description

This function is used for visualization of clustering interaction network plot for the objects that are generated by rhcoclust and list of up-regulated and down-regulated variables list. There are three layers in the network plot, (i) genes (rows) are shown in the first layer, (ii) co-cluster are in the second layer and (iii) columns (compounds) are in the last layer. Red and blue color indicates up and down regulated respectively.

Usage

rhcoclust_internet(data, CoClustObj, CoClust.sig =FALSE,
cex.nodes = 0.7, edge.width = 1)

Arguments

data	A data matrix containing data having the characteristics of interval and ratio level of measurement or continuous data
CoClustObj	A list of output objects from rhcoclust
CoClust.sig	To set no plotting as the default for up and down regulated group. Default is FALSE
cex.nodes	A numerical value giving to control/annotation node size in the network. Default is 0.7.
edge.width	A numerical value giving to control/annotation edge width in the network. Default is 1.

Value

Plot A list up-regulated and down-regulated variables.

Author(s)

Md. Bahadur Badsha <[e-mail]>

See Also

rhcoclust for generating a graph objects for clustering network

Examples

# Load necessary library
library(rhcoclust)
library(fields)

# Load real data
data("FCGE_Data_GMP")
data("FCGE_Data_PPARs")
# Load predefined real data
# Real data use: data <- FCGE_Data_PPARs
# Real data use: data <- FCGE_Data_GMP

# Load predefined simulated data
data("simu_data")

# simulated data
data <- simu_data

# Apply rhcoclust to identify significant co-cluster of samples and their regulatory features
CoClustObj <- rhcoclust(data, rk=4, ck=3, method.dist = "manhattan", method.hclust = "ward.D")
# For real data either FCGE_Data_PPARs or FCGE_Data_GMP
#CoClustObj <- rhcoclust(data, rk=3, ck=3, method.dist = "manhattan", method.hclust = "ward.D")

# Plot interaction network (internet)
# Please use dev.off() to avoid the figure margin from previous plot
# mar order: bottom, left, top, and right
# please use par(mar=c(5,2,5,2)) or modify when necessary to best fit for the plot
Netrhcoclust <- rhcoclust_internet(data, CoClustObj = CoClustObj,
CoClust.sig = FALSE, cex.nodes = 0.7, edge.width = 1)
# Please change or add any parameter if needed.
text(x = -1, y = 1.1, "Row Cluster", cex = 0.7)
# Please change or add any parameter if needed.
text(x = 0, y = 1.1, "Co-Cluster", cex = 0.7)
# Please change or add any parameter if needed.
text(x = 1, y = 1.1, "Column Cluster", cex = 0.7)

mdbahadur/rhcoclust documentation built on Jan. 31, 2023, 10:13 p.m.