network_display: Non-Interactive Network Visualization for INDEED Partial and...

In kg737/INDEED_Patch: Integrated Differential Expression and Differential Network Analysis (INDEED)

Description

A tool to assist in the visualization of the results from INDEED functions patial_cor() and non_partial_cor(). The size and the color of each node can be adjusted by users to represent either the Node_Degree, Activity_Score, Z_Score, or P_Value. The color of the edge is based on the binary value of either 1 corresonding to a positive correlation dipicted as green or a negative correlation of -1 dipicted as red. The user also has the option of having the width of each edge be proportional to its weight value. The layout of the network can also be customized by choosing from the options: 'nice', 'sphere', 'grid', 'star', and 'circle'.

Usage

network_display(results = NULL, nodesize = "Node_Degree",
  nodecolor = "Activity_Score", edgewidth = "NO", layout = "nice")

Arguments

results	This is the result from the calling either partial_cor() or non_partial_cor().
nodesize	This parameter determines what the size of each node will represent. The options are 'Node_Degree', 'Activity_Score', 'Z_Score', and 'P_Value'. The title of the resulting network will identify which parameter was selected to represent the node size. The default is Node_Degree.
nodecolor	This parameter determines what color each node will be, based on a yellow or red color gradient. The options are 'Node_Degree', 'Activity_Score', 'Z_Score', and 'P_Value'. A color bar will be created based on which parameter is chosen.
edgewidth	This is a 'YES' or 'NO' option as to if the edgewidth should be representative of the weight value corresponding to the correlation between two nodes.
layout	User can choose from a a handful of network visualization templates including:'nice', 'sphere', 'grid', 'star', and 'circle'.

Value

A visual dipiction of the network resulting from INDEED functions partial_cor() or non_partial_cor()

Examples

result1 = non_partial_cor(data = Met_GU, class_label = Met_Group_GU, id = Met_name_GU,
                          method = "spearman", permutation_thres = 0.05, permutation = 1000)
network_display(results = result1, layout = 'nice', nodesize = 'Node_Degree',
                nodecolor = 'Activity_Score', edgewidth = 'NO')

kg737/INDEED_Patch documentation built on May 22, 2019, 6:32 p.m.