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Figure 3 | BMC Systems Biology

Figure 3

From: Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease

Figure 3

cor ( K , C ) depends upon network topology and network size. The Spearman correlation (cor(K C); z-axis) between the connectivity and the clustering coefficient as a function of network density (mean node adj. [adjacency]; x-axis) and network size (nodes; y-axis). Signed networks (β = 2) were simulated using the simulateModule function from the WGCNA R package [34]. The seed module eigengene (ME) consisted of 5,000 random, normally distributed features (mean = 0, sd = 1). The function parameters “corPower” and “propNegativeCor” were set to 0.75 and 0, respectively. The function parameter “minCor” was iteratively reduced from .95 to .05 by increments of .05, progressively degrading the strength of node connections; for each iteration, cor(K C) was calculated for module networks of various sizes (n = 10 to 100, by = 10).

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