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  1. IGB
  2. IGBF-3479

Make volcano plots from MvW results

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Create a new markdown that take results from MvW-[assembly].txt and make volcano plots.

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              relates to

              Task - A task that needs to be done. IGBF-3476 Find genes that differ between genotypes are and vf36 again

              • Major - Major loss of function.
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                Mdavis4290 Molly Davis created issue -
                Mdavis4290 Molly Davis made changes -
                Field Original Value New Value
                Epic Link IGBF-3446 [ 22548 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3476 [ IGBF-3476 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                ann.loraine Ann Loraine added a comment - - edited

                Made a prototype RShiny app that reads results and makes a volcano plot. But it is not very good right now.
                It needs a way for users to select the comparison to show. Also, it puts all the SL4 and SL5 genes onto the same plot, which is weird.
                It might be better to show two plots - SL4 and SL5 next to each other.
                Finally, an RShiny app showing just one or two plots makes it difficult to quickly assess all the results. I bet it would be better to write a Markdown that creates all the plots and then just puts them into a multipage PDF, like we did with this paper ages ago: https://pubmed.ncbi.nlm.nih.gov/17369640/

                Unfortunately, however, I can't find the multi-page PDF *or* the code!

                Show
                ann.loraine Ann Loraine added a comment - - edited Made a prototype RShiny app that reads results and makes a volcano plot. But it is not very good right now. It needs a way for users to select the comparison to show. Also, it puts all the SL4 and SL5 genes onto the same plot, which is weird. It might be better to show two plots - SL4 and SL5 next to each other. Finally, an RShiny app showing just one or two plots makes it difficult to quickly assess all the results. I bet it would be better to write a Markdown that creates all the plots and then just puts them into a multipage PDF, like we did with this paper ages ago: https://pubmed.ncbi.nlm.nih.gov/17369640/ Unfortunately, however, I can't find the multi-page PDF * or * the code!
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                ann.loraine Ann Loraine added a comment -

                branch:

                https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3479

                cc: [~molly]

                Show
                ann.loraine Ann Loraine added a comment - branch: https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3479 cc: [~molly]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                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 To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                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
                ann.loraine Ann Loraine made changes -
                Assignee Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Description Create a new markdown that take results from MvW-[assembly].txt and make volcano plots. Create a new markdown that take results from MvW-[assembly].txt and make volcano plots.

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                ann.loraine Ann Loraine added a comment -

                More details on what this task involves:

                • Make a new Markdown that uses code from "DrawPlots.R" to create an HTML or PDF Markdown output file that shows volcano plots for every comparison shown in 72_F3H_PollenTube/results/MvW-SL4.txt and 72_F3H_PollenTube/results/MvW-SL5.txt
                Show
                ann.loraine Ann Loraine added a comment - More details on what this task involves: Make a new Markdown that uses code from "DrawPlots.R" to create an HTML or PDF Markdown output file that shows volcano plots for every comparison shown in 72_F3H_PollenTube/results/MvW-SL4.txt and 72_F3H_PollenTube/results/MvW-SL5.txt
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Merged RShiny app code and new DrawPlots.R into main branch. Proceeding with new Markdown to create volcano plots in "bulk".

                Show
                ann.loraine Ann Loraine added a comment - Merged RShiny app code and new DrawPlots.R into main branch. Proceeding with new Markdown to create volcano plots in "bulk".
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16, Fall 5 [ 180, 181 ] Fall 4 2023 Oct 16, Fall 5, Fall 6 [ 180, 181, 182 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16, Fall 5, Fall 6 [ 180, 181, 182 ] Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7 [ 180, 181, 182, 183 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7 [ 180, 181, 182, 183 ] Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7, Fall 8 [ 180, 181, 182, 183, 184 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7, Fall 8 [ 180, 181, 182, 183, 184 ] Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7 [ 180, 181, 182, 183 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    Mdavis4290 Molly Davis
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                    Dates

                    • Created:
                      Updated: