plotc: Plot the computed clusters igraph.

In camilagazolla/ProKlust: Prokariotic Clustering based on Genome and Sequence Identity/Similarity Matrices

Description

networkD3 library is used to plot the graph and a HTML copy file named network.html is created.

Usage

plotc(igraph, plotFontSize = 10, plotLinkDistance = 60, nodeAttraction = -10)

Arguments

igraph	Obligatory igraph object.
plotFontSize	Optional numeric font size in pixels for the node text labels.
plotLinkDistance	Optional numeric or character string. Either numberic fixed distance between the links in pixels (actually arbitrary relative to the diagram's size). Or a JavaScript function, possibly to weight by Value. For example: linkDistance = JS("function(d)return d.value * 10").
nodeAttraction	Optional numeric value indicating either the strength of the node repulsion (negative value) or attraction (positive value)

Value

The actual plot of the network (an igraph which was transformed into graphical plot by networkD3).

Examples

files <- c("ANIb_percentage_identity.tab", "ANIb_alignment_coverage.tab")
thresholds <- c(0.95, 0.70)
results <- prokluster(filenames = files, cutoffs = thresholds, nodesDictionary = "dictionary.tab")
plottedD3 <- plotc(results$graph)

camilagazolla/ProKlust documentation built on May 22, 2021, 11:10 p.m.