Test

Sample Journal

 

 

<my activity>

Objective

text ...

Time estimated: XXX h; taken XXX h;
Date started: 2020-MM-DD; completed: 2020-MM-DD

Progress

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Activity 1

Notes ...

Activity 2

Notes ...

Conclusion and outlook

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Describe ...

 

(Example Journal Entry) Explore Cytoscape

Objective

Write R code to generate a random network. Explore it with Cytoscape.

Time estimated: 2 h; taken 4 h;
Date started: 2017-09-16; completed: 2017-09-18

Progress

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R code for a random network.

Cytoscape can read networks in SIF format. Wrote the following code to generate N random nodes with random interactions and write them to file.

Expand

My R code below ...

N <- 15  # number of nodes
nMin <- 1 # minimum number of edges
nMax <- 5 # maximum number of edges
OUT <- "myRandomSIF.txt"

# Create N random strings from three uppercase characters
# First make more than we need, because some might not be unique ...
nodes <- character(2*N)

set.seed(161803)
for (i in 1:(2*N)) {
  nodes[i] <- paste0(sample(LETTERS, 1),
                     sample(LETTERS, 1),
                     sample(LETTERS, 1))
}
set.seed(NULL)

nodes <- unique(nodes) # throw away duplicates ...
nodes <- nodes[1:N]    # ... and keep only N

# Create SIF output
mySIF <- character()

set.seed(112358)
for (myA in nodes) {  # for each node
  for (i in 1:sample(nMin:nMax, 1)) { # for a random number of interactors ...
    myB <- sample(nodes, 1)           # ... randomly choose interactor ...
                                      # ... create record and apend to mySIF
    mySIF <- c(mySIF, sprintf("%s\tpp\t%s", myA, myB)) # myA, "pp", myB
                                                       # separated by tabs
  }
}
set.seed(NULL)

# write mySIF to file
writeLines(mySIF, OUT)

Install Cytoscape

Straightforward installation of Cytoscape 3.5.1 from http://www.cytoscape.org

Visualize and explore options

• Worked through an introductory tutorial from http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3.1-part2 Noteworthy: nodes can be coloured by attribute values.

  Loaded my own SIF file with the File → Import → Network → File option. Explored various layout options and visualization styles. Manually added nodes and edges with the options one gets when ctrl-clicking on the canvas.

 

Conclusion and outlook

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• Creating layouts, applying styles, adding nodes and edges with Cytoscape seems straightforward and creates evocative images.
• Analyzing and interpreting the network needs more thought. Need to explore ideas and tools for network analysis next - e.g. clustering tools, enrichment tools, motif discovery ...
• Next: write some code to create attribute values for nodes, import the values, and have Cytoscape style the nodes accordingly.

 

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Notes and References

 

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