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.
rhcoclust_internet(data, CoClustObj, CoClust.sig =FALSE,
cex.nodes = 0.7, edge.width = 1)
Plot A list up-regulated and down-regulated variables.
A data matrix containing data having the characteristics of interval and ratio level of measurement or continuous data
A list of output objects from rhcoclust
To set no plotting as the default for up and down regulated group. Default is FALSE
A numerical value giving to control/annotation node size in the network. Default is 0.7.
A numerical value giving to control/annotation edge width in the network. Default is 1.
Md. Bahadur Badsha <mbbadshar@gmail.com>
rhcoclust for generating a graph objects for clustering network
# 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)
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