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ui.r
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115 lines (112 loc) · 7.29 KB
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####################################################################################################
##### Created by Joseph Longworth
##### Contact josephlongworth@gmail.com
##### This is the UI file for a shiny application providing several tools for Antigen Microarrays
####################################################################################################
# UI - Set-up -----------------------------------------
dashboardPage(
dashboardHeader(title="Antigen Microarray Bioinformatic Pipeline"),
dashboardSidebar(sidebarMenu(
menuItem("Info Page", tabName = "Info_Page", icon = icon("info-circle")),
menuItem("Print Plan Generator", tabName = "Print_Plan_Generator", icon = icon("print")),
menuItem("Scan Data Processing", tabName = "AMDP", icon = icon("grip-vertical")))),
dashboardBody(
tabItems(
# UI - Info Page -----------------------------------------
tabItem(tabName = "Info_Page",
h1("Antigen Microarray Toolset"),
tabBox(width = 12,
tabPanel("Overview",
# box(h2("Overview:"),width = 12,
"This shiny app provides a toolset for production and an analysis of antigen microarrays as described
in", tags$strong("An antigen microarray protocol for COVID-19 serological analysis"), "by Longworth and Dittmar.",
h3("The sidebar to the left navigates between the two activites:"),
tags$ul(tags$li(tags$strong("Print Plan Generator"), " - Used to design and create a print plan for the GeSim Nanoplotter 2.1."),
tags$li(tags$strong("Antigen Array Data Processing")," - Used to import tabulated intensities in Mapix or Genepix format accross multiple gains
fitting the data to a single response variable for each antigen sera comparison.")),
h3("Citation:"),
"To cite the application in publications please use:",
tags$br(),
"Joseph Longworth and Gunnar Dittmar. An antigen microarray protocol for COVID-19 serological analysis. STAR Protocols, Volume 2, Issue 3, 2021. (https://doi.org/10.1016/j.xpro.2021.100815.)"),
tabPanel("Print Plan Generator Instructions",
img(src="Instructions for Print Plan Generator.png",
height = "80%",width = "80%")),
tabPanel("Scan Data Processing Instructions",
img(src="Instructions for Scan Data Processing.png",
height = "80%",width = "80%"))
)
),
# UI - Print Plan Generator -----------------------------------------
tabItem(tabName = "Print_Plan_Generator",
h2("Print Plan Generator"),
box(
title = "Array Parameters", status = "primary", width = 5,
numericInput("Number_of_Samples", label = h3("Number of Antigens"), value = 20,min=1),
splitLayout(cellWidths = c("50%", "50%"),
numericInput("First_sample_well", label = h3("First Well"), value = 1,min=1),
numericInput("Dilution_shift", label = h3("Dilution Shift"), value = 32,min=1)),
splitLayout(cellWidths = c("50%", "50%"),
numericInput("number_of_dilutons", label = h3("Number of Dilutions"), value = 3,min=1),
numericInput("number_of_replicates", label = h3("Number of Replicates"), value = 1,min=1)),
splitLayout(cellWidths = c("50%", "50%"),
numericInput("max_number_of_columns", label = h3("Array Columns"), value = 8),
numericInput("max_number_of_rows", label = h3("Array Rows"), value = 8)),
splitLayout(cellWidths = c("50%", "50%"),
checkboxInput("scramble", label = h3("Scramble?"), value = T),
checkboxInput("Corners", label = h3("Standard Corners?"), value = T))
),
box(
title = "Downloads",width = 7,
splitLayout(cellWidths = c("50%", "50%"),
uiOutput("Download_button1"),
uiOutput("Download_button2"))),
box(
title = "Array Layout",width = 7,
dataTableOutput("Print_Plan_Generator")
),
),
# UI - Antigen Microarray Data Processing (AMDP) -----------------------------------------
tabItem(tabName = "AMDP",
h2("Antigen Microarray Data Processing"),
fluidRow(
column(width = 3,
box(title="New Antigen Microarray Slide",collapsible = TRUE,solidHeader = TRUE,status = "warning", width = NULL,collapsed = TRUE,
h3("Import New Slide"),
splitLayout(cellWidths = c("50%", "50%"),
fileInput('file3', 'Antigen Names' ,accept=c('.xlsx')),
downloadButton("Antigen_Names_Template", label = "Template", class = "btn-info")),
splitLayout(cellWidths = c("50%", "50%"),
fileInput('file2', 'Print Design' ,accept=c('.tab')),
fileInput('file4', 'Scan Data',accept=c('.txt','.gpr'),multiple = T)),
textInput("Slide_Name", "Slide Name:",value = "Slide_Name"),
textInput("Sample_Plate", "Sample Plate:",value = "Sample_Plate"),
selectInput("Immunoglobulin", "Immunoglobulin:",
choices = c("IgG","IgM","IgA","IgE","NA"),multiple = F),
selectInput("Intensity_Metric", "Intensity Metric:",
choices = 'No choices here yet',multiple = F),
numericInput("Gain_Normalisation_Point", "Gain Normalisation Point:",
value = 50,min = 0,max = 100),
actionButton("Process_Import_Data_1", "Process Import Data", class = "btn-success")
),
box(title="Previously Fitted Data Upload",collapsible = TRUE,solidHeader = TRUE,status = "warning", width = NULL,collapsed = TRUE,
fileInput('file5', 'Compiled Dataset Upload',accept=c('.txt')),
actionButton("Process_Import_Data_2", "Process Import Data", class = "btn-success")
)
),
column(width=8,
box( width = NULL,
h3("Import Data"),
plotOutput("Scan_Data_Import"),
actionButton("Apply_Slide_Upload_To_Dataset", "Append", class = "btn-success")
),
box( width = NULL,
h3("Full Dataset"),
"Currently Loaded Data",
splitLayout(cellWidths = c("50%", "50%"),
uiOutput("Download_button3"),
actionButton("Clear_Dataset", "Clear Loaded Dataset",class = "btn-danger", icon = icon("trash-alt"))),
dataTableOutput("Current_Dataset")
)
))
)))
)