QBB2023 - Day 2 - Homework

Instructions

Add each of your answers to /Users/cmdb/qbb2023-answers/day2-homework. Please git push after each update and do not wait until the end of the session e.g.

git add code.py
git add image.png
git commit -m "Add answer for exercise 1, step 1"
git push
# Confirm at github.com

Exercises

  1. Starting with plot-sxl.py, create plot-sisA.py to visualize sisA (FBtr0073461) in a fashion similar to Lott et al 2011 PLoS Biology Fig 3A by adding elements in the following order. After each step, push your code and plot to your git repository and check your repository using the https://github.com web interface (i.e. results in four separate commits).

    • Plot female data
    • Add male data
    • Add 2*male data (HINT: 2 * np.array( y ))
    • Annotate plot (generalize x-axis to 10 not female_10, add title, add x- and y-axis labels)

  2. Modify plot-sisA.py (do not create a new file) to load the transcripts information using open() and a for loop rather than np.loadtxt(). Remember that the first line is a header and should not be stored in the transcripts list. Push just your code to your git repository and confirm at https://github.com that your code no longer uses np.loadtxt().

  3. Recover your original plot-sisA.py using git checkout <commit> plot-sisA.py. Push your code to your git repository and confirm at https://github.com that your code once again uses np.loadtxt().

Additional Exercises

  1. Create plot-fig3a.py that contains a for loop to create individual plots for FBtr0073461, FBtr0070073, and FBtr0077279. Push your code and three plots.

  2. Create plot-fig3a-subplots.py to plot all three transcripts onto a single multipanel plot as in Fig 3A (HINT: plt.subplots(3)). Push your code and new plot.

  3. Complete git-game and git-game-v2.