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Lab2: Animal Network Visualization

Programming Labs will take up to 4 hours and will walk the group through concepts and code that will be useful for future programming and written assignments. While there is a handin, these are marked as completed/not completed, and the solution will be posted to Moodle by the end of the day.

➡️ Lab Day: Tuesday, Sep 8

⭐ Task A: Dolphin Social Network

Before the programming component, we will do a "fast read" of the following paper: Evidence for Social Role in a Dolphin Social Network by David Lusseau. Evolutionary ecology, 2007. We will first read the abstract together.

Spend 15 minutes reading to answer these questions. You won't have all the details, but skimming papers is a useful skill when reading lots of literature.

  1. What is the general hypothesis about animal social behavior that this study aims to test?
  2. Why are bottleneck dolphins useful to study?
  3. There are two behaviors that are noted - what are they and when are they observed?
  4. How was the data collected? Are there any potential biases you see about the data collection?

We will discuss the questions after everyone has had some time looking for answers.

dolphin network Figure 1 from Lusseau paper. Social network of bottlenose dolphins in Doubtful Sound, New Zealand; each vertex represents an individual and each edge represents a pair that was observed in the same school more often than expected by chance; see (26) for more details on how the social network was constructed. Dolphins observed side flopping (SF) are in black and the ones observed upside-down lobtailing (ULT) are in grey.

⭐ Tasks B & C: Post a Test Graph to GraphSpace

GraphSpace is a webserver that allows researchers to interact with networks. It is located at http://graphspace.org/.

⭐ Task B: GraphSpace Preliminaries

First, make an account on GraphSpace: http://graphspace.org/#signup. Use your Reed email for your username, and use something you are OK with sharing for your password (it's easiest to hard-code this in your files).

Once you have an account, click the following link to join the BIO331F20 group:

http://www.graphspace.org/groups/1298/join/?code=0RZ975RD6P

We will be able to share graphs in the class through this group. You should be able to see this graph after joining the group - have you seen it before?

Then, install the graphspace-python library, which allows you to use Python to upload your own graphs to GraphSpace.

  • If you are using Anaconda, you can search for and open the Anaconda Command Prompt and type the following. If you are not using Anaconda and you're on a Mac, you can open a Terminal and type the following:
pip install graphspace_python
  • If you get a permissions error, use sudo, which provides admin access so the package can be installed in the Python directory:
sudo pip install graphspace_python

  • If you get an error that pip is not found and you are using Anaconda, try using pip within a conda environment: here is some documentation.

  • If you get an error that pip is not found and you are not using Anaconda, then try installing pip according to these instructions.

  • If none of these work, ask Anna.

Test that the packages are properly installed by uncommenting Line 10 of lab2.py, replacing 'YOUR EMAIL','YOUR PASSWORD' with your GraphSpace email and password, and running lab2.py without an error. Line 10 establishes a GraphSpace "session", which establishes a connection with the GraphSpace server.

⭐ Task C: Post a Graph to GraphSpace

You will now write a function that will post a test graph to GraphSpace. Documentation for graphspace-python and a cheat sheet for posting graphs will be useful.

Within the post_test_graph() function, complete the following:

  1. Make a small graph with about five nodes and seven edges. Store them as a list of nodes (e.g., ['A','B',...]) and a list of 2-element edges (e.g., [['A','B'],['C','A'],...]). The node names can be anything.

  2. Create a GraphSpace Graph object (we'll call it G) that will be posted to GraphSpace. Set the title and tags of this graph like so:

G = GSGraph()
G.set_name('Test Graph ' + str(time.time()))  ## this name is timestamped
G.set_tags(['Lab 2']) ## tags help you organize your graphs

G is currently empty; we now need to add nodes and edges to it.

  1. Add nodes to your graph G using the G.add_node() function. This function is called on a GraphSpace graph object, and is part of the graphspace_interface library. The function takes a required node ID (a string) and an optional node label (also a string). Use a for loop to add each node n in your node list using the following syntax:
G.add_node(n,label=n)
  1. Add edges to your graph G using the G.add_edge() function using another for loop. This function takes two strings as input, which are simply the edge's node names. For an edge [n1,n2],
G.add_edge(n1,n2)

  1. Now, you are ready to post the graph to GraphSpace. Uncomment the line graph = post(G,graphspace) which will post the graph to GraphSpace. (Note that the post() function handles the case when the graph is brand-new or already exists; it turns out to be pretty slow when replacing a graph, so the timestamp ensures that each graph you upload is "new.")

  2. Finally, add node and edge styles using the options listed on the cheat sheet and user guide. For each node (resp. edge), first add the element and then call add_node_style() (resp. add_edge_style()) a single time for each element. For example,

G.add_node(n,label=n)
G.add_node_style(n,color='red',shape='star',width=80)

HTML colors are allowed, e.g., #73C8F3. You can select node and edge colors using the HTML Color Picker.

⭐ Task D: Post the Dolphin Network to GraphSpace

The Dolphin network described in the Lusseau paper has been parsed into a number of files:

  • dolphin_edgelist.txt - edge list of dolphins by names
  • males.txt females.txt unknown-sex.txt - dolphin names by sex
  • side-floppers.txt - dolphins who had been observed side-flopping
  • upside-down-lobtailers.txt - dolphins who have been observed upside-down lobtailing.

Parse all of this information (the read_onecol() and read_multicols() functions may be useful here). Post the graph to GraphSpace of the dolphin social network annotated by name and sex of each dolphin, as well as whether that dolphin was a side-flopper or upside-down lobtailer. The choice of annotation is up to you (color, size, shape, border, etc.). Add a description of anntations you selected using the set_data() function (HTML formatting allowed):

G.set_data(data={'description': 'females=squares; males=circles; unknown=stars'})

Try out different layouts of the graph. Click the "Change Layout" button to generate the graph using different automatic layouts. Save an automatic or manually generated layout.

Optional: You can also list the node details in the popup argument in the G.add_node() function, and label the nodes with the degree of each node.

Submitting

🌟 You're Done with Tasks A-D! No code handin is required. Instead, you will share your Dolphin network and any saved layouts with the BIO331F20 Group.

  • Share the graph with the group. You can use the share() function provided in lab2.py or share the graph using the website interface (click "share" in the upper right).
  • If you saved any layouts, make sure they are also shared. Click the Layouts tab and select "share" for any layouts you want to share with the group.

Even though you aren't submitting your code here, follow these suggestions:

  • Add comments to your code (this will be useful for posting subsequent graphs).
  • All your code (except import statements and a main() call at the bottom of the file) should be within functions.
  • Clean up your GraphSpace graphs by deleting the unused graphs. On the page that displays all graphs, there is an option to remove each graph you have posted.