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Section 4: Network Visualization using R and Cytoscape – An example
We provide two options for visualizing the changes in associations between a
protein/microRNA hub and its interactors. Typically, the input file for data visualization
will correspond to the output correlation file generated by the function
identifySignificantHubs
(Section 3). For example, if the user was interested in visualizing
the hub-interactor correlations corresponding to the analysis performed in Example 1 of
Section 3, then the input file will be
Test_Output_PPI_Cor.txt
. However, to illustrate our
data visualization function, we consider input files that are already available in the
Example dataset (Section 2).
Option 1: Visualization in R
For an analysis involving two conditions, we can visualise a single hub of interest
together with its interactors,
e.g.
the gene “ABL1” along with its interactors, by typing at
the R command prompt
visualizeNetwork(inputFile="Gene_Output_1_Cor.txt"
, inputHub="ABL1"
, paletteVector=c("red", "yellow", "green"))
For an explanation of the data file to be provided as input, refer Section 9. Similarly, for
an example visualization of a microRNA and its interactome, at the R command prompt
type
visualizeNetwork(inputFile="Micro_Output_1_Cor.txt"
, inputHub="hsa-miR-551a"
, paletteVector=c("red", "yellow", "green"))
For an analysis involving multiple conditions, we can visualise a single hub of interest
together with its interactors for exactly two conditions,
e.g.
the gene “ABL1” along with
its interactors in States B and C, by typing at the R command prompt
visualizeNetwork(inputFile="Gene_Output_2_Cor.txt"
, inputHub="ABL1"
, paletteVector=c("red", "yellow", "green")
, condVector = c("StateB", "StateC"))
Option 2: Visualization in Cytoscape
For visualization in Cytoscape, we can use (i) the output file containing the hub-
interactor pairs or (ii) a subset of this file. The advantage of using the subset is that it
allows us to focus on only the significant hubs. To obtain the subset, at the R command
prompt type
Summary of Contents for GLSY22522
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