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| + | Test: timestamp is 2020-09-16 04:19:42 |
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| − | <div class="b1">
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| − | Sample Journal
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| − | </div>
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| − | {{Vspace}}
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| − | <!-- A table of contents will replace the __TOC__ "magic text" -->
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| − | __TOC__
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| − | {{Vspace}}
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| − | <!-- =================== BEGIN of template for one entry =================== -->
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| − | == <my activity> ==
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| − | ;Objective
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| − | : text ...
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| − | <div class="time-estimate">
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| − | Time estimated: XXX h; taken XXX h;<br/>
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| − | Date started: 2020-MM-DD; completed: 2020-MM-DD
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| − | </div>
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| − | '''Progress'''
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| − | ----
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| − | ;Activity 1
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| − | : Notes ...
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| − | ;Activity 2
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| − | : Notes ...
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| − | '''Conclusion and outlook'''
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| − | ----
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| − | Describe ...
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| − | {{Vspace}}
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| − | <!-- ==================== END of template for one entry ==================== -->
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| − | <!-- ========================== BEGIN sample entry ========================= -->
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| − | | |
| − | == (Example Journal Entry) Explore Cytoscape ==
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| − | ;Objective
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| − | : Write R code to generate a random network. Explore it with Cytoscape.
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| − | <div class="time-estimate">
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| − | Time estimated: 2 h; taken 4 h;<br/>
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| − | Date started: 2017-09-16; completed: 2017-09-18
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| − | </div>
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| − | '''Progress'''
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| − | ----
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| − | ;R code for a random network.
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| − | : Cytoscape can read networks in [http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats#SIF_format SIF format]. Wrote the following code to generate N random nodes with random interactions and write them to file.
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| − | <div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
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| − | My R code below ...
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| − | <div class="mw-collapsible-content">
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| − | N <- 15 # number of nodes
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| − | nMin <- 1 # minimum number of edges
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| − | nMax <- 5 # maximum number of edges
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| − | OUT <- "myRandomSIF.txt"
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| − | # Create N random strings from three uppercase characters
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| − | # First make more than we need, because some might not be unique ...
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| − | nodes <- character(2*N)
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| − | set.seed(161803)
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| − | for (i in 1:(2*N)) {
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| − | nodes[i] <- paste0(sample(LETTERS, 1),
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| − | sample(LETTERS, 1),
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| − | sample(LETTERS, 1))
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| − | }
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| − | set.seed(NULL)
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| − | nodes <- unique(nodes) # throw away duplicates ...
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| − | nodes <- nodes[1:N] # ... and keep only N
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| − | | |
| − | # Create SIF output
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| − | mySIF <- character()
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| − | set.seed(112358)
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| − | for (myA in nodes) { # for each node
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| − | for (i in 1:sample(nMin:nMax, 1)) { # for a random number of interactors ...
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| − | myB <- sample(nodes, 1) # ... randomly choose interactor ...
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| − | # ... create record and apend to mySIF
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| − | mySIF <- c(mySIF, sprintf("%s\tpp\t%s", myA, myB)) # myA, "pp", myB
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| − | # separated by tabs
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| − | }
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| − | }
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| − | set.seed(NULL)
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| − | # write mySIF to file
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| − | writeLines(mySIF, OUT)
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| − | </div>
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| − | </div>
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| − | | |
| − | ;Install Cytoscape
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| − | : Straightforward installation of <b>Cytoscape 3.5.1</b> from http://www.cytoscape.org
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| − | ;Visualize and explore options
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| − | *: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.
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| − | *: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.
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| − | {{Vspace}}
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| − | '''Conclusion and outlook'''
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| − | ----
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| − | * Creating layouts, applying styles, adding nodes and edges with Cytoscape seems straightforward and creates evocative images.
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| − | * 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 ...
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| − | * Next: write some code to create attribute values for nodes, import the values, and have Cytoscape style the nodes accordingly.
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| − | <!-- =========================== END sample entry ========================== -->
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| − | {{Vspace}}
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| − | ----
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| − | <!-- Footnotes -->
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| − | ==Notes and References==
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| − | <references />
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| − | {{Vspace}}
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| − | <!-- Category and Footer -->
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| − | [[Category:BCH441-2020_Journal]]
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| − | ----
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| − | {{CC-BY}}
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| − | <!-- END -->
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