bioFabric: BioFabric for R
In wjrl/RBioFabric: BioFabric network visualization tool

Description Usage Arguments Details Author(s) References Examples

View source: R/bioFabric.R

An R implementation of the BioFabric network visualization tool

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  bioFabric(inGraph, userOrder = NULL, orderFunc = NULL,
    shadowLinks = FALSE, dropNodeLabels = FALSE,
    dropZoneLabels = FALSE)

`inGraph`	The graph to plot, in igraph format (see `igraph`). Node names should already be set using the vertex attribute "name", though the attribute "label" will work as well. If not set, the function will assign names of the form "BFn".
`userOrder`	(optional) An ordered list specifying the ordering of the node rows in the plot; nodes are identified using node name. All nodes must be present in the list. If this list is provided, the default node ordering routine will not be used.
`orderFunc`	(optional) A function that takes a graph to plot and returns the graph with the nodes reordered in the desired node order. Providing the defaultNodeOrder function for this parameter gives the default behavior. Note that if this parameter is provided, the userOrder parameter is ignored.
`shadowLinks`	(optional) Default value is FALSE. If set to TRUE, BioFabric will display shadow links. See the BioFabric paper or blog for more info.
`dropNodeLabels`	(optional) Default value is FALSE. If set to TRUE, no node labels are displayed. With large networks, some PDF readers cannot correctly handle tiny text, and labels may need to be dropped.
`dropZoneLabels`	(optional) Default value is FALSE. If set to TRUE, no node zone labels are displayed. With large networks, some PDF readers cannot correctly handle tiny text, and labels may need to be dropped.

Plots a network, provided in igraph format (see igraph), using BioFabric. This release supports user-specified node orders and the display of shadow links.

Best results are obtained using a PDF display target, as shown in the example. BioFabric is very sensitive to correct relative scaling of linewidth, label size, and grid size. The PDF output has been targeted for correctly handling this scaling. PNG output should also be acceptable.

SIZING: As the network grows, you will need to increase the size of the output to be able to get per-link resolution. PDF files that are not big enough (e.g. only 10 inches wide) will create links below the hairline limit and may not print well. PNG outputs are the better bet to create low-resolution images of large networks in page-size dimensions. To be able to view an enormous network and zoom to see each link, create an enormous PDF file (e.g. 40, 80, 100+ inches wide!) or PNG file (e.g. 30,000 pixels wide if the network has 5000 links).

VIEWERS: PDF or PNG viewers that cannot do antialiasing of line art are a poor choice for BioFabric networks. The closely spaced parallel lines of a BioFabric plot MUST be antialiased to get acceptable results. Some specific viewer notes:

Evince on Linux for PDF (Document Viewer 2.30.3 tested): Antialiased is fixed on, and visuals are good. Problems: Very tiny text below some size threshold explodes to a huge size. Cannot zoom above 400 to explore network. No drag hand cursor to navigate, which is essential. Note that for Postscript output, Evince does not antialias, giving very poor results.

Preview on Mac for PDF (Version 4.2 tested): Be sure that "Anti-alias text and line art" is checked on the PDF tab for Preferences, which gives fair visuals. Good maximum zoom level, and the Move cursor provides convenient draggable navigation.

Adobe Reader on Mac for PDF (Version 9.5.5 tested): Be sure that "Smooth line art" is checked, and "Enhance thin lines" is NOT checked, on the Page Display Preferences. The Hand tool is available via Tools->Select & Zoom->Hand Tool, and the maximum 6400 percent zoom level is good for exploration.

RStudio (0.97 tested): You won't be able to see much in the tiny Plot Frame. Due to a known RStudio issue, the Zoom window does not provide correct label sizing or line width sizing, since the plots are scaled based on the Plot Frame dimensions. Use the PDF or PNG output routes for now.

General note on image viewers: If you have a plot with 10,000 links, you are quickly heading towards PNG images that are over 32,000 pixels wide for high resolution. Lots of image viewers start to get cranky when viewing images that are more than 32,000 pixels wide.

If you want to explore large networks with BioFabric, best to export the network as a tab-delimited SIF file and use the Java-based BioFabric application, which is designed for interactive large network visualization and exploration.

Bill Longabaugh <wlongabaugh@systemsbiology.org>

Home page: http://www.BioFabric.org

Blog: http://biofabric.blogspot.com

Paper: http://www.biomedcentral.com/1471-2105/13/275

## Not run: 
# Gotta have igraph!

library(igraph)

# Generate graph

bfGraph = barabasi.game(100, m=6, directed=FALSE)

# Plot it up! For best results, make the PDF in the same
# aspect ratio as the network, though a little extra height
# covers the top labels

height <- vcount(bfGraph)
width <- ecount(bfGraph)
aspect <- height / width;
plotWidth <- 10.0
plotHeight <- plotWidth * (aspect * 1.2)
pdf("myBioFabricOutput.pdf", width=plotWidth, height=plotHeight)
bioFabric(bfGraph)
dev.off()

## End(Not run)