Adding Plotly feature to MSstatsPTM with Error Handling

[deril2605]

Adding new Plotly library to MSstatsPTM to render Plotly plots back to MSstatsShiny app. The new parameter isPlotly to dataProcessPlotsPTM and groupComparisonPlotsPTM function handles this. If isPlotly is set to FALSE, it behaves normally (renders ggPlots).

In git diff, all the lines in the files appears to be changed. Devon and I identified this problem as issues with line endings. Below is a possible approach to fix it

There is this homebrew package dos2unix that converts file endings to what we need. Here is a test that I did

• I created a copy branch devel called test-1 and applied this dos2unix package on R/dataProcessPlotsPTM.R https://github.com/Vitek-Lab/MSstatsPTM/compare/devel...test-1?expand=1 It shows all the lines have changed because we have converted the line endings
• Then I created another branch test-2 which is checked out from test-1 and then made a small line change to verify git recognizes only that line has changed and it works https://github.com/Vitek-Lab/MSstatsPTM/compare/test-1...test-2?expand=1
• Thus, we need to modify all the R files on the devel branch using dos2unix and then checkout into the feature branch to make changes