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geanders / csu_msmb

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Updated post for exercise solution 2.3 #40

Closed serewilliams closed 4 years ago

serewilliams commented 4 years ago

Thank you for all of your helpful comments! I am now well versed on the 'hypen' vs. 'en-dash' or even the 'em-dash'. (How nice that both of the non-hyphen options use hyphens.)

I attempted the fork using the new code in the shell. Good news is that it ran! I'm not sure it worked, though. Here is what returned: image

geanders commented 4 years ago

@serewilliams : Wonderful! I think we're on the right track.

I know exactly what to do with your current error message. You just need to go to the "Git" window in RStudio for the project and commit any changes you have there. Most of the ones coming up seem to be in the "public" file. Commits and changes to those are no problem, because they get rewritten every time you serve the site, so they'll easily sync up with the current content. You have one file to commit in the ".Rproj" directory. I'm not sure what that one is... Go ahead and commit it, too, and if it seems to cause any problems in the main website, I can fix it when we merge in your pull request for your post.

Once you've committed your local changes, re-run from the bash shell: 

git pull upstream master

And I think we should be good with your updates.

I haven't gotten a chance yet to look through your part c code to look for the bug and help with that, but will try to before class.

Also, I've updated the posts on making a vocab list and an exercise to fix that typo and to tell other students about where to save data files they need for their markdown. Hopefully our troubleshooting here will help the next students to try this!

serewilliams commented 4 years ago

Ok, I was able to commit those changes and then run the script in the shell. Do I need to pull/push for submit a pull request again?

On Thu, Feb 20, 2020 at 8:33 AM Brooke Anderson notifications@github.com wrote:

@serewilliams https://github.com/serewilliams : Wonderful! I think we're on the right track.

I know exactly what to do with your current error message. You just need to go to the "Git" window in RStudio for the project and commit any changes you have there. Most of the ones coming up seem to be in the "public" file. Commits and changes to those are no problem, because they get rewritten every time you serve the site, so they'll easily sync up with the current content. You have one file to commit in the ".Rproj" directory. I'm not sure what that one is... Go ahead and commit it, too, and if it seems to cause any problems in the main website, I can fix it when we merge in your pull request for your post.

Once you've committed your local changes, re-run from the bash shell:

git pull upstream master

And I think we should be good with your updates.

I haven't gotten a chance yet to look through your part c code to look for the bug and help with that, but will try to before class.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/geanders/csu_msmb/pull/40?email_source=notifications&email_token=AHQOHZXGUTTYNJ3X3D3UCSTRD2PFBA5CNFSM4KYHZLP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMOW3JI#issuecomment-589131173, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHQOHZSBTZVVIX4LO5AJ5YDRD2PFBANCNFSM4KYHZLPQ .

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Seré Williams, M.S.

PhD Student

Program in Cell & Molecular Biology

Colorado State University, Fort Collins, CO

Name Pronunciation: Sir-ee

Tel: 303.550.4375

E-mails: sere.a.williams@gmail.com, sere.williams@colostate.edu

geanders commented 4 years ago

Yes, you will need to push your local changes to your Github repository (you can use the up arrow in the RStudio GitHub pane for that) and then submit a pull request on GitHub just like you did before.

geanders commented 4 years ago

Great, I've merged in those changes, and they all look great! So I think now we're just down to the "part c" section, right?

serewilliams commented 4 years ago

Yup, I think so.

On Thu, Feb 20, 2020 at 12:27 PM Brooke Anderson notifications@github.com wrote:

Great, I've merged in those changes, and they all look great! So I think now we're just down to the "part c" section, right?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/geanders/csu_msmb/pull/40?email_source=notifications&email_token=AHQOHZWKDNYGKNIC4QJE3YTRD3KSBA5CNFSM4KYHZLP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMPX2KI#issuecomment-589266217, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHQOHZX4UCZ2QG7FOEEWFODRD3KSBANCNFSM4KYHZLPQ .

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Seré Williams, M.S.

PhD Student

Program in Cell & Molecular Biology

Colorado State University, Fort Collins, CO

Name Pronunciation: Sir-ee

Tel: 303.550.4375

E-mails: sere.a.williams@gmail.com, sere.williams@colostate.edu

geanders commented 4 years ago

Okay, so looking at part c, here are a few comments: 

codon_compared <- mtb %>% 
  group_by(AmAcid) %>% 
  mutate(total = sum(Number),
         n_codons = n(),
         expected = total / n_codons)

You can convince yourself that you've gotten this right by rerunning your column barchart with these expected values: 

ggplot(codon_compare, aes(x=Codon, y=expected)) +
     geom_col()+
     facet_wrap(~AmAcid, scales="free") +
     theme(axis.text.x = element_text(angle = 45, hjust = 1))

Take a look at these suggestions and see if they provide a path forward for you, and then I'm happy to check back in!