Callouts call attention to the neighborhoods around SRSF2 and NTRK1. (A) Reconstruction of Fig 5A from Preston and colleagues, which contains the largest subnetwork resulting from a pathway and enrichment analysis. The authors also used different node shapes to distinguish among complexes, proteins, and processes, and different line and line ending styles to indicate the relationship among the nodes. In this Cytoscape (Cytoscape Consortium ) recreation of Fig 3 from Morris and colleagues, the authors used several different marks to explain the data in the network, including stars to indicate highly mutated nodes (in addition to the color gradient) and a red circle to indicate the subject of one of the scenarios outlined in the paper. Use other visual marks and channels appropriately. Both images were created with Cytoscape (Cytoscape Consortium ) and postprocessed using Photoshop (Adobe ) to assemble them. (B) shows an improved version, including a legend and appropriate and separate quantitative colormaps for edges and nodes. The colormap also groups unrelated edges and nodes together through similar colors, whereas the node labels in light gray have low luminance contrast with the white background and are difficult to read. (A) is a recreation of the original Fig 3B shown in the paper, including the color-blind and saturated color scheme, which makes it difficult to perceive the relative importance of the nodes. Two network images based on data from Khaled and colleagues. PPI, protein–protein interaction.Įxample aggregation using data from Kuhner and colleagues, which replicates the sequence of steps described in Gehlenborg and colleagues, from a hardly readable network (A), gradually through (B) and (C), to a legible, aggregated version of the same network (D).
#Cytoscape multiple edges software#
The two images have been generated using the open-source software Porgy ( ). (B) The same network, but this time the layout has been improved to make better use of the available space, resulting in larger labels. (A) An example network based on PPI data from Andrei and colleagues, in which the node labels are too small to be legible. Structural connectivity strength is encoded by the gray-level color scale of the edges.
Symmetry and spatial positions are approximately reproduced. Instead, the second layout in the right image is driven by the spatial relation of brain regions, generating automatically a "flattened" mouse brain representation as seen from above. The left image uses connectivity strength as the driving force for the layout, posing strongly connected nodes closely together, but at the same time neglecting the spatial context of the network. The illustrations have been generated using the Cytoscape.js (Cytoscape Consortium ) implementation of the force-directed layout algorithm CoSE. The data are derived from the Allen Mouse Brain Connectome dataset. This figure shows two illustrations representing the same region of the normalized structural mouse brain connectivity data set described by Ganglberger and colleagues. These images were produced in Cytoscape (Cytoscape Consortium ) with the clusterMaker2 app and postprocessed in Photoshop (Adobe ) to merge in the insets.īeware of unintended spatial interpretations. Notice how difficult it is to see the close interaction between the nodes, even in the inset in this second image, due to the clutter resulting from other nodes. The image on the right (B) is of the same data depicted as a node-link diagram with the same nodes highlighted. The inset within the image shows a cluster identified on the diagonal that represents the exosome complex. The image on the left (A) shows an adjacency matrix representation of the network. These two images represent the same data from Collins and colleagues. GBM, glioblastoma multiforme PPI, protein–protein interaction. The colors represent the fold change for subtype 3 of GBM, the node sizes vary with the number of mutations, and the edges represent functional associations. In the right image (B), a PPI network was created using the Cytoscape stringApp and annotated with data downloaded from TCGA.
The node color represents the overall variance of expression across a set of patients, and the lines and arrows represent the function of the interactions between the proteins. The left image (A) shows a curated cancer signaling pathway taken from the TCGA's original Mondrian plugin to Cytoscape (Cytoscape Consortium ). Two representations of proteins involved in GBM. First, determine the figure purpose and assess the network.
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