Nothing
R/cal_ui.R
In LFApp: Shiny Apps for Lateral Flow Assays
Defines functions
cal_ui
cal_ui <- function(request) {
tagList(
fluidPage(
theme = shinytheme("sandstone"),
useShinyjs(),
titlePanel("LFA App calibration"),
tags$style(type='text/css', "#stop { float:right; }"),
actionButton("stop", "Quit App"),
tabsetPanel(id = "tabs",
## Start of Tab Image Editor
tabPanel("Cropping and Segmentation", value = "tab1",
sidebarLayout(
sidebarPanel(
radioButtons("upload",
label = ("Upload Image or Choose Sample"),
choices = list("Upload Image" = 1,
"Sample Image" = 2),
selected = 1),
conditionalPanel(
condition = "input.upload == 1",
fileInput(inputId = 'file1',
label = 'Upload Image',
placeholder = 'JPEG, PNG, and TIFF are supported',
accept = c(
"image/jpeg",
"image/x-png",
"image/tiff",
".jpg",
".png",
".tiff"))
),
uiOutput("rotatePanel"),
hr(style="border-color: black"),
h5("Set number of strips and number of lines per strip",
style="font-weight:bold"),
sliderInput("strips", "Number of strips:",
min = 1, max = 10, value = 1),
sliderInput("bands", "Number of lines:",
min = 2, max = 6, value = 2),
),
mainPanel(
h3('Cropping and Segmentation', align = "center"),
plotOutput("plot1",
click = "plot_click",
dblclick = "plot_dblclick",
hover = "plot_hover",
brush = "plot_brush"),
br(),
h6("Click and drag to select a region of interest. Double click on the selected region to zoom.", align = "center"),
br(),
column(6,
actionButton("reset", label = "Reset"),
tags$style(type='text/css', "#reset { display: block; width:70%; margin-left: auto; margin-right:auto;}"),
),
column(6, shinyjs::disabled(
actionButton("segmentation", label = "Apply Segmentation")),
tags$style(type='text/css', "#segmentation { display: block; width:70%; margin-left: auto; margin-right:auto;}"),
)
)
)
), # END OF TAB PANEL
## Start of Tab Background Correction
tabPanel("Background", value = "tab2",
sidebarLayout(
sidebarPanel(
numericInput(inputId = "selectStrip",
label = "Select strip:",
value = 1,
min = 1,
max = 1,
step = 1,
width = NULL
),
hr(style="border-color: black"),
h5("Select threshold method",
style="font-weight:bold"),
radioButtons("colorImage",
label = ("Color image?"),
choices = list("No" = 1,
"Yes" = 2),
selected = 1),
conditionalPanel(
condition = "input.colorImage == 2",
radioButtons("channel",
label = ("Conversion mode"),
choices = list("luminance",
"gray",
"red",
"green",
"blue"),
selected = "luminance")
),
radioButtons("invert",
label = ("Lines are darker than background?"),
choices = list("No" = FALSE,
"Yes" = TRUE),
selected = FALSE),
radioButtons("thresh",
label = ("Threshold method"),
choices = list("Otsu" = 1,
"Quantile" = 2,
"Triangle" = 3,
"Li" = 4),
selected = 1),
conditionalPanel(
condition = "input.thresh == 3",
numericInput(inputId = "tri_offset",
label = "Offset:",
value = 0.2,
min = 0,
max = 1,
step = 0.01,
width = NULL)
),
conditionalPanel(
condition = "input.thresh == 2",
numericInput(inputId = "quantile1",
label = "Probability [%]:",
value = 99,
min = 0,
max = 100,
step = 0.1,
width = NULL
)
),
actionButton("threshold", label = "Apply Threshold"), br(),
hr(style="border-color: black"),
actionButton("data", label = "Add To Intensity Data"), br(),
hr(style="border-color: black"),
actionButton("showIntensData", label = "Switch To Intensity Data")
),
mainPanel(
HTML(
paste(
h3('Background Correction', align = "center"),
verbatimTextOutput("thresh"),br(),
h4('Signal Intensity Above Background', align = "center"),
plotOutput("plot3"),
h4('Lines After Background Subtraction', align = "center"),
plotOutput("plot4"),
verbatimTextOutput("meanIntens"),
verbatimTextOutput("medianIntens"),
'<br/>','<br/>'
)
),
width = 8
)
)
), # END OF TAB PANEL
## Start of Tab Data
tabPanel("Intensity Data", value = "tab3",
sidebarLayout(
sidebarPanel(
h5("You can also upload existing intensity data and go to experiment info", style="font-weight:bold"),
fileInput("intensFile", "Select CSV file",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")), hr(style="border-color: black"),
h5("Download intensity data", style="font-weight:bold"),
downloadButton("downloadData", "Download Data"), br(),
hr(style="border-color: black"),
actionButton("expInfo", label = "Switch To Experiment Info"),
hr(style="border-color: black"),
h5("For restart with new data", style="font-weight:bold"),
actionButton("deleteData", label = "Delete Data"), br(),
),
mainPanel(
DTOutput("intens")
)
)
), # END OF TAB PANEL
tabPanel("Experiment Info", value = "tab4",
sidebarLayout(
sidebarPanel(
h5("Upload experiment info or upload existing merged data and go to calibration", style="font-weight:bold"),
fileInput("expFile", "Select CSV file",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
# Input: Checkbox if file has header ----
checkboxInput("header", "Header", TRUE),
# Input: Select separator ----
radioButtons("sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
# Input: Select quotes ----
radioButtons("quote", "Quote",
choices = c(None = "",
"Double Quote" = '"',
"Single Quote" = "'"),
selected = '"'), hr(style="border-color: black"),
h5("Select ID columns and merge datasets", style="font-weight:bold"),
textInput("mergeIntens", label = "ID Column Intensity Data", value = "File"),
textInput("mergeExp", label = "ID Column Experiment Info", value = "File"),
actionButton("merge", label = "Merge With Intensity Data"), br(),
hr(style="border-color: black"),
h5("Download merged data", style="font-weight:bold"),
# actionButton("refreshData2", label = "3) Refresh Data"), br(), br(),
downloadButton("downloadData2", "Download Data"), br(),
hr(style="border-color: black"),
actionButton("prepare", label = "Prepare Calibration"),
hr(style="border-color: black"),
h5("For restart with new data", style="font-weight:bold"),
actionButton("deleteData2", label = "Delete Data"), br(),
),
mainPanel(
DTOutput("experiment")
)
)
), # END OF TAB PANEL
tabPanel("Calibration", value = "tab5",
sidebarLayout(
sidebarPanel(
textInput("folder", "Specify a folder for the analysis results", value=file.path(fs::path_home(), "Documents/LFApp"),
placeholder=file.path(fs::path_home(), "Documents/LFApp")),
hr(style="border-color: black"),
# h5("Optional: average technical replicates", style="font-weight:bold"),
# hr(style="border-color: black"),
# h5("Optional: reshape data from long to wide", style="font-weight:bold"),
# hr(style="border-color: black"),
h5("You can also upload existing data and run the calibration", style="font-weight:bold"),
fileInput("prepFile", "Select CSV file",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
hr(style="border-color: black"),
radioButtons("radioPrepro",
label = ("Further preprocessing steps:"),
choices = list("None" = 1,
"Average technical replicates" = 2,
"Reshape from long to wide" = 3),
selected = 1),
conditionalPanel(
condition = "input.radioPrepro == 2",
hr(style="border-color: black"),
textInput("combRepsColSI", label = "Column with sample information:", value = "Sample"),
numericInput(inputId = "colorsBands",
label = "Number of analytes/colors per line:",
value = 1,
min = 1,
max = 5,
step = 1,
width = NULL
),
conditionalPanel(
condition = "input.colorsBands > 1",
textInput("combRepsColCL", label = "Column with color information:", value = "Color"),
),
radioButtons("radioReps",
label = ("Choose measure for averaging:"),
choices = list("Mean" = 1,
"Median" = 2),
selected = 1),
actionButton("combReps", label = "Average Technical Replicates"),
),
conditionalPanel(
hr(style="border-color: black"),
condition = "input.radioPrepro == 3",
textInput("reshapeCol", label = "Column:", value = "Color"),
actionButton("reshapeWide", label = "Reshape"),
),
hr(style="border-color: black"),
h5("Download calibration data", style="font-weight:bold"),
# actionButton("refreshData3", label = "3) Refresh Data"), br(), br(),
downloadButton("downloadData3", "Download Data"),
hr(style="border-color: black"),
h5("Calibration", style="font-weight:bold"),
textInput("analysisName", label = "Analysis name:", value = "Model1"),
radioButtons("chosenModel",
label = "Choose model:",
choices = list("Linear model (lm)" = 1,
"Local polynomial model (loess)" = 2,
"Generalized additive model (gam)" = 3),
selected = 1),
selectInput("concVar", "Select column with concentration", choices = ""),
checkboxInput("useLog", "Logarithmize concentration", value=FALSE),
textAreaInput("respVar", label = "Specify the response variable (R expression)"),
textAreaInput("subset", label = "Optional: specify subset (logical R expression)"),
actionButton("runCali", label = "Run Calibration Analysis"),
hr(style="border-color: black"),
h5("For restart with new data", style="font-weight:bold"),
actionButton("deleteData3", label = "Delete Data"), br(),
),
mainPanel(
DTOutput("calibration")
)
)
), # END OF TAB PANEL
tabPanel("Results", value = "tab6",
sidebarLayout(
sidebarPanel(
h4("Open analysis report"),
actionButton("openReport", label = "Open")
),
mainPanel(
h3("Results of Calibration Analysis", style="font-weight:bold"), br(),
h4("Calibration model", style="font-weight:bold"),
verbatimTextOutput("modelSummary"), br(),
plotOutput("plot5"), br(),
verbatimTextOutput("LOB"),
verbatimTextOutput("LOD"),
verbatimTextOutput("LOQ")
)
)
) # END OF TAB PANEL
) # END OF TAB SET PANEL
)
)
}
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LFApp documentation built on Nov. 6, 2023, 5:08 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions cal_ui
cal_ui <- function(request) {
tagList(
fluidPage(
theme = shinytheme("sandstone"),
useShinyjs(),
titlePanel("LFA App calibration"),
tags$style(type='text/css', "#stop { float:right; }"),
actionButton("stop", "Quit App"),
tabsetPanel(id = "tabs",
## Start of Tab Image Editor
tabPanel("Cropping and Segmentation", value = "tab1",
sidebarLayout(
sidebarPanel(
radioButtons("upload",
label = ("Upload Image or Choose Sample"),
choices = list("Upload Image" = 1,
"Sample Image" = 2),
selected = 1),
conditionalPanel(
condition = "input.upload == 1",
fileInput(inputId = 'file1',
label = 'Upload Image',
placeholder = 'JPEG, PNG, and TIFF are supported',
accept = c(
"image/jpeg",
"image/x-png",
"image/tiff",
".jpg",
".png",
".tiff"))
),
uiOutput("rotatePanel"),
hr(style="border-color: black"),
h5("Set number of strips and number of lines per strip",
style="font-weight:bold"),
sliderInput("strips", "Number of strips:",
min = 1, max = 10, value = 1),
sliderInput("bands", "Number of lines:",
min = 2, max = 6, value = 2),
),
mainPanel(
h3('Cropping and Segmentation', align = "center"),
plotOutput("plot1",
click = "plot_click",
dblclick = "plot_dblclick",
hover = "plot_hover",
brush = "plot_brush"),
br(),
h6("Click and drag to select a region of interest. Double click on the selected region to zoom.", align = "center"),
br(),
column(6,
actionButton("reset", label = "Reset"),
tags$style(type='text/css', "#reset { display: block; width:70%; margin-left: auto; margin-right:auto;}"),
),
column(6, shinyjs::disabled(
actionButton("segmentation", label = "Apply Segmentation")),
tags$style(type='text/css', "#segmentation { display: block; width:70%; margin-left: auto; margin-right:auto;}"),
)
)
)
), # END OF TAB PANEL
## Start of Tab Background Correction
tabPanel("Background", value = "tab2",
sidebarLayout(
sidebarPanel(
numericInput(inputId = "selectStrip",
label = "Select strip:",
value = 1,
min = 1,
max = 1,
step = 1,
width = NULL
),
hr(style="border-color: black"),
h5("Select threshold method",
style="font-weight:bold"),
radioButtons("colorImage",
label = ("Color image?"),
choices = list("No" = 1,
"Yes" = 2),
selected = 1),
conditionalPanel(
condition = "input.colorImage == 2",
radioButtons("channel",
label = ("Conversion mode"),
choices = list("luminance",
"gray",
"red",
"green",
"blue"),
selected = "luminance")
),
radioButtons("invert",
label = ("Lines are darker than background?"),
choices = list("No" = FALSE,
"Yes" = TRUE),
selected = FALSE),
radioButtons("thresh",
label = ("Threshold method"),
choices = list("Otsu" = 1,
"Quantile" = 2,
"Triangle" = 3,
"Li" = 4),
selected = 1),
conditionalPanel(
condition = "input.thresh == 3",
numericInput(inputId = "tri_offset",
label = "Offset:",
value = 0.2,
min = 0,
max = 1,
step = 0.01,
width = NULL)
),
conditionalPanel(
condition = "input.thresh == 2",
numericInput(inputId = "quantile1",
label = "Probability [%]:",
value = 99,
min = 0,
max = 100,
step = 0.1,
width = NULL
)
),
actionButton("threshold", label = "Apply Threshold"), br(),
hr(style="border-color: black"),
actionButton("data", label = "Add To Intensity Data"), br(),
hr(style="border-color: black"),
actionButton("showIntensData", label = "Switch To Intensity Data")
),
mainPanel(
HTML(
paste(
h3('Background Correction', align = "center"),
verbatimTextOutput("thresh"),br(),
h4('Signal Intensity Above Background', align = "center"),
plotOutput("plot3"),
h4('Lines After Background Subtraction', align = "center"),
plotOutput("plot4"),
verbatimTextOutput("meanIntens"),
verbatimTextOutput("medianIntens"),
'<br/>','<br/>'
)
),
width = 8
)
)
), # END OF TAB PANEL
## Start of Tab Data
tabPanel("Intensity Data", value = "tab3",
sidebarLayout(
sidebarPanel(
h5("You can also upload existing intensity data and go to experiment info", style="font-weight:bold"),
fileInput("intensFile", "Select CSV file",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")), hr(style="border-color: black"),
h5("Download intensity data", style="font-weight:bold"),
downloadButton("downloadData", "Download Data"), br(),
hr(style="border-color: black"),
actionButton("expInfo", label = "Switch To Experiment Info"),
hr(style="border-color: black"),
h5("For restart with new data", style="font-weight:bold"),
actionButton("deleteData", label = "Delete Data"), br(),
),
mainPanel(
DTOutput("intens")
)
)
), # END OF TAB PANEL
tabPanel("Experiment Info", value = "tab4",
sidebarLayout(
sidebarPanel(
h5("Upload experiment info or upload existing merged data and go to calibration", style="font-weight:bold"),
fileInput("expFile", "Select CSV file",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
# Input: Checkbox if file has header ----
checkboxInput("header", "Header", TRUE),
# Input: Select separator ----
radioButtons("sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
# Input: Select quotes ----
radioButtons("quote", "Quote",
choices = c(None = "",
"Double Quote" = '"',
"Single Quote" = "'"),
selected = '"'), hr(style="border-color: black"),
h5("Select ID columns and merge datasets", style="font-weight:bold"),
textInput("mergeIntens", label = "ID Column Intensity Data", value = "File"),
textInput("mergeExp", label = "ID Column Experiment Info", value = "File"),
actionButton("merge", label = "Merge With Intensity Data"), br(),
hr(style="border-color: black"),
h5("Download merged data", style="font-weight:bold"),
# actionButton("refreshData2", label = "3) Refresh Data"), br(), br(),
downloadButton("downloadData2", "Download Data"), br(),
hr(style="border-color: black"),
actionButton("prepare", label = "Prepare Calibration"),
hr(style="border-color: black"),
h5("For restart with new data", style="font-weight:bold"),
actionButton("deleteData2", label = "Delete Data"), br(),
),
mainPanel(
DTOutput("experiment")
)
)
), # END OF TAB PANEL
tabPanel("Calibration", value = "tab5",
sidebarLayout(
sidebarPanel(
textInput("folder", "Specify a folder for the analysis results", value=file.path(fs::path_home(), "Documents/LFApp"),
placeholder=file.path(fs::path_home(), "Documents/LFApp")),
hr(style="border-color: black"),
# h5("Optional: average technical replicates", style="font-weight:bold"),
# hr(style="border-color: black"),
# h5("Optional: reshape data from long to wide", style="font-weight:bold"),
# hr(style="border-color: black"),
h5("You can also upload existing data and run the calibration", style="font-weight:bold"),
fileInput("prepFile", "Select CSV file",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
hr(style="border-color: black"),
radioButtons("radioPrepro",
label = ("Further preprocessing steps:"),
choices = list("None" = 1,
"Average technical replicates" = 2,
"Reshape from long to wide" = 3),
selected = 1),
conditionalPanel(
condition = "input.radioPrepro == 2",
hr(style="border-color: black"),
textInput("combRepsColSI", label = "Column with sample information:", value = "Sample"),
numericInput(inputId = "colorsBands",
label = "Number of analytes/colors per line:",
value = 1,
min = 1,
max = 5,
step = 1,
width = NULL
),
conditionalPanel(
condition = "input.colorsBands > 1",
textInput("combRepsColCL", label = "Column with color information:", value = "Color"),
),
radioButtons("radioReps",
label = ("Choose measure for averaging:"),
choices = list("Mean" = 1,
"Median" = 2),
selected = 1),
actionButton("combReps", label = "Average Technical Replicates"),
),
conditionalPanel(
hr(style="border-color: black"),
condition = "input.radioPrepro == 3",
textInput("reshapeCol", label = "Column:", value = "Color"),
actionButton("reshapeWide", label = "Reshape"),
),
hr(style="border-color: black"),
h5("Download calibration data", style="font-weight:bold"),
# actionButton("refreshData3", label = "3) Refresh Data"), br(), br(),
downloadButton("downloadData3", "Download Data"),
hr(style="border-color: black"),
h5("Calibration", style="font-weight:bold"),
textInput("analysisName", label = "Analysis name:", value = "Model1"),
radioButtons("chosenModel",
label = "Choose model:",
choices = list("Linear model (lm)" = 1,
"Local polynomial model (loess)" = 2,
"Generalized additive model (gam)" = 3),
selected = 1),
selectInput("concVar", "Select column with concentration", choices = ""),
checkboxInput("useLog", "Logarithmize concentration", value=FALSE),
textAreaInput("respVar", label = "Specify the response variable (R expression)"),
textAreaInput("subset", label = "Optional: specify subset (logical R expression)"),
actionButton("runCali", label = "Run Calibration Analysis"),
hr(style="border-color: black"),
h5("For restart with new data", style="font-weight:bold"),
actionButton("deleteData3", label = "Delete Data"), br(),
),
mainPanel(
DTOutput("calibration")
)
)
), # END OF TAB PANEL
tabPanel("Results", value = "tab6",
sidebarLayout(
sidebarPanel(
h4("Open analysis report"),
actionButton("openReport", label = "Open")
),
mainPanel(
h3("Results of Calibration Analysis", style="font-weight:bold"), br(),
h4("Calibration model", style="font-weight:bold"),
verbatimTextOutput("modelSummary"), br(),
plotOutput("plot5"), br(),
verbatimTextOutput("LOB"),
verbatimTextOutput("LOD"),
verbatimTextOutput("LOQ")
)
)
) # END OF TAB PANEL
) # END OF TAB SET PANEL
)
)
}
Try the LFApp package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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