Module Network Plot

Visualizes the top hub genes for selected modules as a circular network plot with one inner circle and one outer circle.

I have looked back to the tutorial and know that there are two softwares VisANT and Cytoscape performed to visualize the network, but just between genes in each module and clinical traits. Can anyone guide me to visualize the network of genes in each module or point out the tutorial for that purpose? Thanks in advance.

Here we can see what one of these network plots looks like In this network, each node represents a gene, and each edge represents the co-expression relationship between two genes in the network. Each of these module network plots are colored based on the color column in the hdWGCNA module assignment table GetModulesseurat_obj.

8.b Topological overlap matrix plot for visualizing the network pological overlap matrix supplemented by hierarchical c ustering dendrograms and the module colors. For large gene s

Hi Sam, I have another question. Even after re-installing scWGCNA, quotModuleNetworkPlotquot does not seem producing any plots using Zhou data as well as my own. It gives an output like this , but not pl

Please take a look here A Exporting WGCNA step-to-step network construction objects into igraph object Once you have your WGCNA data as an igraph object, plotting the network is as simple as using the base plot function.

Weighted gene co-expression network analysis WGCNA is a powerful all-in-one analysis method that allows biologists to understand the transcriptome-wide relationships of all genes in a system rather than each gene in isolation. WGCNA enables the identification of clusters modules of features that exhibit correlated patterns and the assessment of the relationship between distinct clusters

ModuleNetworkPlot Description Visualizes the top hub genes for selected modules as a circular network plot with one inner circle and one outer circle. Usage ModuleNetworkPlot seurat_obj, n_inner 10, n_outer 15, n_conns 500, mods quotallquot, outdir quotModuleNetworksquot, wgcna_name NULL, plot_size c6, 6, edge.alpha 0.25, edge.width 1, vertex.label.cex 1, vertex.size 6

3hdWGCNA - jianshu.com hdWGCNA modulemodulehubGO

The WGCNA R software is a collection of R functions for performing various aspects of weighted correlation network analysis 14. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, data visualization, and interfering with external software.