ui.R

# This is the user-interface definition of a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com
#

library("shiny")

shinyUI(fluidPage(


  # Sidebar with a slider input for number of bins
  verticalLayout(
    titlePanel("AlignStat: A tool for the statistical comparison of alternative multiple sequence alignments"),

    wellPanel(
      div(class="header",
        p("This webtool compares two alternative multiple sequence alignments (MSAs) to determine how well 
          they align homologous residues in the same columns as one another. It classifies similarities 
          and differences into conserved sequence, conserved gaps, splits, merges and shifts. 
          Summarising these categories for each column yields information on which columns are agreed 
          upon by both MSAs, and which differ. Output graphs visualise the comparison data for analysis."),
        p("All of the calculations and plots generated by this webtool can also be generated using the underlying ",
          a(href="https://github.com/TS404/AlignStat","AlignStat R package")," which is available on ",
          a(href="https://cran.r-project.org/package=AlignStat","CRAN"),"")
      )
    ),
        
    conditionalPanel(
      condition = "!output.comparison_done",
      mainPanel(
        h3("Upload your two alignments to make a comparison"),
        p("Alignments must be in fasta, clustal, msf, or phylip formats. Both alignments should contain the same sequences in any order."),
        p("If you are unsure how to format your inputs or simply want some data to try the app please take a look at the example data."),
        a(href="https://dl.dropboxusercontent.com/u/226794/AlignStatShiny/example.zip",class="btn btn-default shiny-download-link",
          list(tags$em(class="fa fa-download"),"Example Data")),
        br(),br(),
        wellPanel(
          fileInput("align_a","Alignment A in fasta, clustal, msf, or phylip format"),
          fileInput("align_b","Alignment B in fasta, clustal, msf, or phylip format"),
          checkboxInput("stack_category_proportions","Stack category proportions",value = TRUE),
          checkboxInput("show_prop_cys","Show cysteine abundance",value = FALSE),
          checkboxInput("calculate_column_score","Calculate column score",value = FALSE),
          checkboxInput("calculate_sum_of_pairs","Calculate sum of pairs",value = FALSE)
        )
      )      
    ),

    conditionalPanel(
      condition = "output.comparison_done",
      h3("Your AlignStat results are shown below. To run a new comparison simply refresh this page in your browser")
    ),
    
    conditionalPanel(
      condition = "output.comparison_done",
      wellPanel(
        # Show a plot of the generated distribution
        plotOutput("heatmap"),
        textOutput("heatmap_caption"),
        downloadButton("heatmap_download",label = "Download")
      )
    ),

    conditionalPanel(
      condition = "output.comparison_done",
      wellPanel(
        plotOutput("matrix"),
        textOutput("matrix_caption"),
        downloadButton("matrix_download",label = "Download")
      )
    ),
    
    conditionalPanel(
      condition = "output.comparison_done",
      wellPanel(
        plotOutput("match_summary"),
        textOutput("match_summary_caption"),
        downloadButton("match_summary_download",label = "Download")
      )
    ),

    conditionalPanel(
      condition = "output.comparison_done",
      wellPanel(
        plotOutput("plot_dissimilarity_summary"),
        textOutput("plot_dissimilarity_caption"),
        downloadButton("dissimilarity_summary_download",label = "Download")
      )
    ),
    
    conditionalPanel(
      condition = "output.comparison_has_sum_of_pairs",
      wellPanel(
        plotOutput("SP_summary"),
        textOutput("SP_summary_caption"),
        downloadButton("SP_summary_download",label = "Download")
      )   
    ),    


    conditionalPanel(
        condition = "output.comparison_done",
        wellPanel(
          p("When comparing the positions of two MSAs:
            A ‘match’ is when both alignments contain an identical characters that is not a gap.
            A ‘merge’ is when alignment A contains a gap, but alignment B contains any other character.
            A ‘split’ is when alignment B contains a gap, but alignment A contains any other character.
            A ‘shift’ is when two alignments contain a non-identical character, neither of which are gaps.
            A ‘conserved gap’ is when the both alignments contain a gap."),
          p("For further information see",
            a(href="https://github.com/TS404/AlignStat","github.com/TS404/AlignStat"))
        ),
        wellPanel(
          h4("Download results in csv format"),
          downloadButton("similarity_matrix_csv","Similarity Matrix"),
          downloadButton("dissimilarity_matrix_csv","Dissimilarity Matrix"),
          downloadButton("results_summary_csv","Results Summary"),
          p("The Similarity Matrix records which columns of the reference and comparison
            MSAs best match. Its [i,j]th entry is the similarity score between
            the ith column of the reference alignment and the jth column of the
            comparison alignment. Used to determine which columns are most similar
            for further analysis. Used to generate the similarity heatmap plot."),
          p("The Dissimilarity Matrix categorises dissimilarity in the MSF.
            Its [i,j]th entry is the dissimilarity category of the jth
            residue of the ith sequence for the reference alignment versus the
            comparison alignment (M=match, g=conserved gap, m=merge, s=split, x=shift).
            Used to the dissimilarity matrix plot."),        
          p("The Results Matrix summarises columnwise similarity and disimilarity.
            Its [i,j]th entry is the ith match category average of the
            jth column of the reference alignment versus the comparison alignment
            (i1=match, i2=conserved gap, i3=merge, i4=split, i5=shift). Used to
            generate the similarity summary and dissimilarity summary plots.")
        )
    ),


    conditionalPanel(
      condition = "output.comparison_has_sum_of_pairs",
      wellPanel(
        h4("Download SPS results in txt and formats"),
        downloadButton("SP_ref_txt","Sum of Pairs Reference"),
        downloadButton("SP_com_txt","Sum of Pairs Comparison"),
        downloadButton("SP_scores_csv","Sum of Pairs Scores"),
        p("The Sum of Pairs Reference lists all residue pairs present in the reference
          MSA. The Sum of Pairs Comparison lists all residue pairs present in the
          comparison MSA. The Sum of Pairs Scores lists the proportion of reference
          pairs retained in each column of the comparison MSA")        
      )   
    ),    


    wellPanel(
        p("AlignStat was developed by Thomas Shafee and Ira Cooke at the ",
          a(href="http://www.latrobe.edu.au/lims","La Trobe Institute of Molecular Science (LIMS)")," and ",
            a(href="http://hexima.com.au/","Hexima")),
        img(src="http://cysbar.science.latrobe.edu.au/img/lims.png",width="200px"),
        img(src="http://cysbar.science.latrobe.edu.au/img/hexima.png",width="200px")
    )

  )
))