hw08 ready for grading

[mylinhthibodeau]

Dear colleagues,

My repository for homework 8 is here. Here are the files to review for my homework 8 Shiny App:

• My online Shiny App Genomics Disorders Exploration
• My Shiny App files
  • File User Interface (UI)
  • File Server
  • Folder data
  • Folder www
• Since medical genetics/genomics is specialized topic, I made a tutorial for you to test my app and it can be found both in the Genomic Disorders Exploration App and at the end of the README file.
• Extensive data manipulation/transformation was required to obtain correctly formatted datasets for the app, so I have a dedicated Rmd/Md file for data manipulation here.

Let me know if you have any questions, Warm regards, My Linh Thibodeau

[mylinhthibodeau]

Dear @mattsada, dear @vmichalowski,

I just fixed the hyperlink to my Shiny App. You most likely won't even notice because you didn't get to my app yet, but just in case, I thought I would mention it.

I hope you will enjoy reviewing my homework !

Don't forget to check out the tutorial, but please note it's a work in progress and there might be some mistakes as I didn't update the tutorial after some late bug fixes. Don't hesitate to point out these mistakes to me and of course, you can also go wild and explore the app on your own terms as well :)

Warm regards, My Linh

[mattssca]

Hi @mylinhthibodeau and thanks for the invite!

Wow, this is amazing I'm very impressed with the app that you've developed and you demonstrate excellent programming skills, as well as a thorough understanding of the material 🥇 . Your code is concise and easy to follow, and yes, thanks for all the helpful annotations within your code it helps the peer-reviewer a lot! with that being said, here's my peer review of your efforts.

• Your README is documented very well and it's gives a perfect overview of your development process, as well as aid in navigating your extensive repository.

• I especially like your Newly acquired skills or knowledge and I will defiantly consider constructing a similar section in my own, future work.

• It's very nice of you to include a tutorial and I think you did an awesome job in explaining some key points, like "Why this app?" and "What does it do so far?"

• I had a great time exploring your app and I couldn't fin any major flaws, so the things that I point out in this peer review should be considered as minor suggestions for improvement or common feedback .

• It's obvious that you put a lot of efforts in developing this app and I think the outcome was a perfect demonstration of your understanding of how to make use of the shiny app spectra of R Studio.

• Keep in mind that it's not necessary to load all of your packages in both the UI and the SERVER scripts, one is sufficient.

• Also, you have included neat functions such as a download button, links and images in your final app, which really improves the overall impression of your app.

• I like your Final Notes section. Besides demonstrating that you are an ambitious student, it reflects that you really have given this app a lot of thought in terms of how you could improve it.

• Your sixth tab doesn't seem to have a description in your README file in the What does it do so far section.

Overall, I think you did everything (and more!) that was requiRed from you in this assignment and I wish you all the luck with your future assignments. Have a nice weekend and I'll see you in class.

[vmichalowski]

Hi @mylinhthibodeau

Wow, excellent work on this assignment! It's clear that you went above and beyond what was expected to create something that you care about and plan to actually work on beyond this class assignment. I just have a few points of feedback for you:

• Very original app idea!
• Nice work experimenting with feautures beyond what was covered in class. Everything that you tried to implement was functional when I played around with the app. The tutorial was very helpful too. My one suggestion for easing navigation flow would be to consider using a drop down menu instead of a box where the user types in the phenotype in tab 1 - that way the user would know what their options.
• I also liked that you played around with the tabs feature, but I also wonder whether it would make sense to have tab one and two all in one tab instead - without instructions, it might be confusing to navigate to different tabs to enter input.
• Considering the code you had to use for this app was quite extensive, you did a great job organizing the different components, in that it was easy for me to see why each peice of code was there and what it was meant to do.

Excellent work overall!

Victoria

[ksedivyhaley]

App uses ui.R and server.R file: Yes Deployed online: Yes Course repo includes README, code: Yes Acknowledge datset source: Yes New app or 3+ added features: Yes (new app, at least 4 new features) Reflection: Yes

Comments:

• Impressive use of a complicated dataset, especially considering how much work went into preparing the data. Good observations regarding the difficulties in the process!
• I'm not actually seeing any results at the end of your tutorial scenario 1 – and pearlman syndrome doesn't appear to be in your dataset. You also say I should expect 7 entries from scenario 2 when I see 4. Did you do some additional data cleaning/filtering after writing the tutorial?
• It's not clear whether the second and third panels are using each others' filtering parameters.
• The layout is a little confusing in general. You might consider combining the “phenotype and frequency,” “check out this checkbox”, and “add organ selection” tabs into one tab with multiple options for interacting with the data – just stick the “specific mutation consequence” checkbox and “target organ” drop-down under the frequency selection buttons. The “all phenotypes” tab might also belong in “overview of source data” instead of the “Examples of phenotype choices” section.
• I like how you've included the tutorial both in the README and in the app itself.
• Code is well commented
• Since your Tab 4 plots do not depend on any user input, you could produce and save them in your Rmd file and then just add them to the shiny app rather than render plots interactively. This would probably be more computationally efficient.
• I hope you enjoy continuing to work on the app. Adding “contains the term” to the first tab would be very useful – you should be able to implement it using regular expressions and string pattern matching.
• Good luck to your friend on her exam!

Your mark will be distributed later. If you would like more feedback, please feel free to message me on slack.