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Jasmine Dumas edited this page Oct 1, 2015 · 9 revisions

To-Do list for Fall 2015 work for shinyGEO

  1. Limit the GSE numbers available to the user. The user should only be able to download series corresponding to experiments containing expression profiles. This way the user cannot mistakenly download an inappropriate dataset (such as a methylation dataset). It should be straightforward to get the accession numbers from GEO. Then instead of a text box we'd use a drop-down box for the user to select the series to download. Update: This is done. However, we want an option to override this so that a user can download a GSE number not in the list. We will also need a way to periodically update the lists using the scripts in platforms/ and series/. We will need to discuss this at a later date. ✅

  2. Prevent the user from downloading GSE series that are "too large", as that will cause the tool to freeze currently (I'm not sure how to do this currently). We'd want to look at if there's a way to get the size of a file from the internet without downloading it).

  3. If there is only 1 (appropriate) platform for a dataset, that should be downloaded automatically and the user need not select it. Update: See Jasmine's e-mail. This can be accomplished using devtools::install_github('yihui/shiny@bugfix/selectize-selected') Note: By the time this tasks is needed, the development version of DT should be fixed and therefore the devtools version of Yihui's repo will not be needed in a separate call.

  4. If there are multiple platforms for the dataset, the user should be given additional information about the platforms – the easiest thing to do at this point would be to link to the platform on GEO, and let the user look and decide. Ideally, we could also select the platform based on the gene the user was interested in. (Since not all genes are available on all platforms). Users will be disappointed if they download a platform only to find out that the gene of interest is not available. However, knowing whether the gene is available requires downloading the platform, so it is a catch-22. I think including links to the platforms is the best way to go currently. Update: This is done, however this is not as necessary as previous since the drop down boxes include some information about the platforms. Instead of the platform button, it may be better to include a 'View on GEO' button that has links to the series as well as the platform(s). ✅

  5. In the time/outcome column selection, clicking on a column highlights the column and selects it. However, using the drop down box does not highlight the column. That needs to be added.

  6. Automate the selection of the time and outcome columns for survival analysis. When the user wants to select the columns, prior to seeing the table one of the following will happen:

    1. Shiny displays a message saying that our tool has identified the following columns that might contain survival information, displays the columns and how shiny will parse those columns by default. If the user agrees, they simply hit continue. If they disagree or choose to, they can look at the full table.

    2. Shiny displays a message saying that survival and time columns could not be automatically detected, and the user is told to make the selection manually.

  7. The user should be able to change the colors on the KM curves. ✅

  8. Allow the user to generate reports with knitR and shinyAce

  9. If a gene symbol column cannot be found in the selected platform, allow users to view platform data and select the appropriate gene/probe column to analyze. ✅

  10. Limit the number of columns that can be selected at anytime (1 column for differential expression, 2 for survival analyses). This will have to managed by observing the number of selected columns and if updating it accordingly. For example, if a column is already selected under the differential expression analysis, selection of a new column should (a) add that column to the drop down box and (b) remove (unhighlight) the previously selected column.

  11. Investigate color, shiny themes, ECSU color theme for the application -- there is already a branch, called shiny themes designated for this experiment in color/branding ✅

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