Week 2

###Here are my tasks from the proposal for week 2:

Task: Create a routine for pre-processing of the downloaded data set to provide the user with the ability to edit the data to account for for either long sample names, heterogeneous mixing of columnar data, and mis-spellings which can lead to a lot of time spent manually “cleaning” the data and incorrect graphics.

Method: Incorporate the DataTables Extension for editing information within the table; Incorporate the DataTables Editor options to allow for truncation of sample names into manageable descriptions and correcting spelling errors. This feature will decrease time to clean the data, and allow for a wider range of data sets that can be used for survival analysis which not currently available outside of current R packages as a suite of tools.

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June 1

• I met with my mentor today @ 9AM and showed him my progress with converting the DT package and it was well received! We discussed and debugged some of the errors I was getting in regards to using a reactive expression with the data object in the following code:

  dd = clinicalDataSummary()

  action = dataTableAjax(session, data=dd, rownames = TRUE) # for the row_output as characters

• I learned a important lesson in software development today from my mentor. Make it work in an example, then iterate the new features into your existing code (to ultimately see where errors arise). I had the right idea, and have been testing out new features with a small app (that I build up to refresh my memory of shiny development) that uses the mtcars dataset but I couldn't get the row selection to be the actual rowname / character value and instead outputs the row index number. After reading the documentation and interpreting the errors being from a "this is something you tried to do that can only be done within a reactive expression" we figured out that the entire output$clinicalDataSummary ... needed to be wrapped in a observe({}). Now to just get that to populate the drop-down menus!

• Next for this week is trying to come up with a intuitive way of allowing a user to edit the full clinical data table (ie. data cleaning preparation for survival analysis).

• Also after reloading the application I think the jQuery gets wonky from the selection = 'single' option for the datatable widget.

June 7

• I have been bogged down with Homework and completing my final but this week I was able to have the drop-down populated with the single row selection for the clinical summary table!

• My goal for this week is to still work on the editing capabilities for the full data table for week 3 since the week 3 tasks of gene isolation has already been completed (from the original starter template). More to come soon