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  1. IGB
  2. IGBF-3481

Make and deploy shiny app that displays gene expression profile using a barplot

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          As also described in IGBF-3449 (see early comments) we need a fast way for a researcher to view a barplot showing the expression profile across all samples for a given gene. This is important because we need to be able to quickly sanity check the results from statistical analyses, time course clustering, etc.

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              Task - A task that needs to be done. IGBF-3449 Investigate: Make Rshiny app that plots data for a given gene

              • Major - Major loss of function.
              • Closed

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-3446 [ 22548 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3449 [ IGBF-3449 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16 [ 180 ]
                ann.loraine Ann Loraine made changes -
                Description As also described in IGBF-3449 (see early comments) we need a fast way for a researcher to view a barplot showing the expression profile across all samples for a given gene. This is important because we need a fast, quick way to sanity check the results from statistical analyses, time course clustering, etc.

                		As also described in IGBF-3449 (see early comments) we need a fast way for a researcher to view a barplot showing the expression profile across all samples for a given gene. This is important because we need to be able to quickly sanity check the results from statistical analyses, time course clustering, etc.

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                ann.loraine Ann Loraine added a comment -

                See linked ticket for comments on barplot app. We created it (initially) as a proof-of-concept for the linked ticket.

                Show
                ann.loraine Ann Loraine added a comment - See linked ticket for comments on barplot app. We created it (initially) as a proof-of-concept for the linked ticket.
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                ann.loraine Ann Loraine added a comment - - edited

                For review, see comment from linked ticket, copied here:

                Hi Molly Davis!

                I am pushing a new branch to my fork with my barplot code.

                A couple of changes:

                The new code supports both SL4 and SL5.
                I changed the y axis label to include the string "(scaled counts)"
                See:

                https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3449-1

                Note that because the above work started as part of a different ticket, the branch name uses the name of the other ticket instead of this one.

                Show
                ann.loraine Ann Loraine added a comment - - edited For review, see comment from linked ticket, copied here: Hi Molly Davis! I am pushing a new branch to my fork with my barplot code. A couple of changes: The new code supports both SL4 and SL5. I changed the y axis label to include the string "(scaled counts)" See: https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3449-1 Note that because the above work started as part of a different ticket, the branch name uses the name of the other ticket instead of this one.
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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                Mdavis4290 Molly Davis added a comment -

                Review:

                • I ran the app on my computer and it works perfectly with SL4 and SL5 genes.
                • Only comment is we might want to name our app scripts differently if we are going to add multiple to the repo.

                Ready for PR!

                Show
                Mdavis4290 Molly Davis added a comment - Review : I ran the app on my computer and it works perfectly with SL4 and SL5 genes. Only comment is we might want to name our app scripts differently if we are going to add multiple to the repo. Ready for PR!
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                I am going to rename the app to avoid name conflict and then submit a PR.

                Show
                ann.loraine Ann Loraine added a comment - I am going to rename the app to avoid name conflict and then submit a PR.
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                ann.loraine Ann Loraine added a comment -

                Changes:

                Show
                ann.loraine Ann Loraine added a comment - Changes: Changed branch name to match this ticket: https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3481 Renamed app.R to BarplotApp.R to avoid conflicts with other apps under development and for clarity
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                ann.loraine Ann Loraine added a comment -

                PR submitted and merged into main. Ready for testing.

                Show
                ann.loraine Ann Loraine added a comment - PR submitted and merged into main. Ready for testing.
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16 [ 180 ] Fall 4 2023 Oct 16, Fall 5 [ 180, 181 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
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                Mdavis4290 Molly Davis added a comment - - edited

                Testing:

                • Running the app on my machine and had no issues with it launching
                • SL4 and SL5 gene names both work now with the app
                • I did run into an error under certain conditions. If the SL5 gene name has NA as the description it throws this error: missing value where TRUE/FALSE needed. Might need to add code that deals with this occurrence and fill the title with something else like "Unknown protein" or something like that.

                Moving back to To Do!

                Show
                Mdavis4290 Molly Davis added a comment - - edited Testing : Running the app on my machine and had no issues with it launching SL4 and SL5 gene names both work now with the app I did run into an error under certain conditions. If the SL5 gene name has NA as the description it throws this error: missing value where TRUE/FALSE needed . Might need to add code that deals with this occurrence and fill the title with something else like "Unknown protein" or something like that. Moving back to To Do !
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
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                ann.loraine Ann Loraine added a comment - - edited

                Fixed the bug. Tested a gene Solyc10G001086 that has "NA".
                Also, added more info the display. Now it says what genome assembly the gene came from.
                Redeployed to https://ann-loraine-gmail.shinyapps.io/barplot/

                Show
                ann.loraine Ann Loraine added a comment - - edited Fixed the bug. Tested a gene Solyc10G001086 that has "NA". Also, added more info the display. Now it says what genome assembly the gene came from. Redeployed to https://ann-loraine-gmail.shinyapps.io/barplot/
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Hide
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                Mdavis4290 Molly Davis added a comment -

                Tested the new redeployed app and the error is gone! Thank you!

                Moving to done!

                Show
                Mdavis4290 Molly Davis added a comment - Tested the new redeployed app and the error is gone! Thank you! Moving to done!
                Mdavis4290 Molly Davis made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Mdavis4290 Molly Davis made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Ann Loraine [ aloraine ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    • Created:
                      Updated:
                      Resolved: