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MicCheck.R
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MicCheck.R
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library(shiny)
library(stringr)
library(shinyjs)
# Read in our metadata file
Metadata = read.delim(
"Metadata_new.txt",
header = TRUE,
stringsAsFactors = FALSE,
quote = "",
sep = "\t",
na = ""
)
examples = read.delim(
"examples_new.txt",
header = TRUE,
stringsAsFactors = FALSE,
quote = "",
sep = "\t",
na = ""
)
#Get of Na values in the examples and replace them with a blank space
Nalist <- c("None","NONE", "NA", "N/A", "n/a","na", "No example")
for (i in 1:length(examples)){
if (examples[i] %in% Nalist){
examples[i] <- gsub(paste(Nalist, collapse = '|'), " ", examples[i])
}
}
#examples <- gsub(paste(Nalist, collapse = '|'), " ", examples)
#For outputting checkboxes in app:
checkBox = "☐ "
#function for making the .tsv contents into checklist output:
appendChecklist <- function(input, myCol, showExamples) {
output <- ""
if(showExamples==TRUE){
for (i in 1:length(myCol)) {
output <- paste(output, checkBox, na.omit(Metadata[[myCol]]), " ", "<em style=color:CornflowerBlue>", na.omit(examples[[myCol]]), "</em>", "<br>")
#output <- append(output, paste(checkBox, na.omit(Metadata[[myCol]]), " ", "<em style=color:CornflowerBlue>", na.omit(examples[[myCol]]), "</em>", "<br>"))
}
}
else{
for (i in 1:length(myCol)) {
output <- paste(output, checkBox, na.omit(Metadata[[myCol]]), "<br>")
#output <- append(output, paste(checkBox, na.omit(Metadata[[myCol]]), "<br>"))
}
}
finalOutput <- append(input,output)
return(str_replace_all(finalOutput,"\"",""))
}
checkNull <- function(input){
if(!is.null(input)){
return(input)
}
else{
return("no_input")
}
}
getModalityName <- function(input){
if (!is.null(input)) {
if (input == "WF") {
scope = "Widefield"
}
else if (input == "SConfocal") {
scope = "Spinning Disk Confocal"
}
else if (input == "PConfocal") {
scope = "Laser-scanning Confocal"
}
else if (input == "MPhoton") {
scope = "Multiphoton"
}
else{
scope = "Microscope"
}
}
return(scope)
}
sortItems <-function(str_list){
sortedlist <- c()
hold <- c()
for(item in str_list){
if(grepl("***", item, fixed=TRUE)){
hold <- append(hold, item)
}
else{
sortedlist <- append(sortedlist, item)
}
}
return(append(sortedlist,hold))
}
#note: requires pander library, #install.packages(pander), (tinytex library) #install.packages("tinytex") #tinytex::install_tinytex()
# If your .tsv file is displaying with quotes around the text, this is likely something excel did. Copy paste into notepad and save again and it should work.
# Cannot use xelatex on shiny.io
#~~~~~~~~~~~~~~~~~
# User interface
#~~~~~~~~~~~~~~~~~
ui <- fluidPage(
useShinyjs(),
titlePanel("Microscopy Metadata Checklist Generator (MicCheck)"),
sidebarLayout(
sidebarPanel(
helpText("For more information, see Montero-Llopis et al., 2021."),
####################
#Questions
####################
# Q1: Modality
radioButtons(
"Q1",
"1. Which image modality are you using?",
c(
"Widefield" = "WF",
"Spinning Disk Confocal" = "SConfocal",
"Point Scanning Confocal" = "PConfocal",
"Multiphoton" = "MPhoton"
),
selected = character(0)
),
# Q1b: WF wheels/cubes
checkboxGroupInput(
"Q1b",
"Did you use excitation/emission filter wheels or filter cubes?",
choiceNames = list("Filter Wheel", "Filter Cube"),
choiceValues = list("wheel", "cube"),
selected=character(0)
),
# Q1c: WF laser vs LED
checkboxGroupInput(
"Q1c",
"What light source(s) did you use to illuminate your sample?",
choiceNames = list("Non-laser light source (e.g., LED, metal halide)", "Lasers"),
choiceValues = list("LEDs", "Lasers"),
selected=character(0)
),
# Q2: Uni-meta-related
radioButtons(
"Q2",
"2. Did you acquire transmitted light images (e.g., phase contrast, brightfield, DIC)?",
c("Yes" = "Y",
"No" = "N"),
selected = character(0)
),
radioButtons(
"Q3",
"3. Did you use additional magnification (e.g., optovar, relay lens)?",
c("Yes" = "Y",
"No" = "N"),
selected = character(0)
),
# Application-related
checkboxGroupInput(
"Q4",
"4. Did you perform any of these multidimensional acquisitions?",
choiceNames = list("Multi-color", "Z-stack", "Time-lapse"),
choiceValues = list("multi-color", "z-stack", "time-lapse")
),
radioButtons(
"Q5",
"5. Did you do a multi-point acquisition (e.g., revisiting different positions in a time-lapse)?",
c("Yes" = "Y", "No" = "N"),
selected = character(0)
),
radioButtons(
"Q6",
"6. Did you do tiling, scan large area, or mosaic acquisition?",
c("Yes" = "Y", "No" = "N"),
selected = character(0)
),
radioButtons(
"Q7",
"7. Did you do live cell imaging?",
c("Yes" = "Y",
"No, my sample is fixed" = "N"),
selected = character(0)
),
checkboxGroupInput(
"Q8",
"8. What kind of fluoropohore(s) did you use in your sample?",
choiceNames = list("Fluorescent protein", "Fluorescent dye/organic dye"),
choiceValues = list("FP", "Dye")
),
radioButtons(
"Q9",
"9. Did you use any transfection reagents to express the fusion protein of interest in your sample?",
c("Yes" = "Y", "No" = "N"),
selected = character(0)
),
radioButtons(
"Q10",
"10. Did you use use microscopes in a core facility?",
c("Yes" = "Y", "No" = "N"),
selected = character(0)
),
helpText("App developed by Rebecca Senft (2021)."),
width = 5
),
####################
# Main Panel
####################
mainPanel(
#Styles:
tags$head(tags$style("#newline{font-size: 10px;")),
tags$head(
tags$style(
"#title{color: black;
font-size: 20px;
font-style: bold;
text-align: center;
}"
)
),
tags$head(
tags$style(
"#c1,#c2,#c3,#c4,#c5,#c5,#c6,#c7,#c8,#cModality{color: white;
font-style: bold;
background-color: black;
text-align: center;
}"
)
),
# Checklist output:
htmlOutput("title"),
#htmlOutput("newline"),
helpText("***Asterisks indicate optional items."),
textOutput("c1"),
htmlOutput("Stand_motorized"),
textOutput("cModality"),
htmlOutput("nonWF_Stand_motorized"),
textOutput("c2"),
htmlOutput("Illumination"),
textOutput("c3"),
htmlOutput("WaveSelection"),
textOutput("c4"),
htmlOutput("Optics"),
textOutput("c5"),
htmlOutput("Detector"),
textOutput("c6"),
htmlOutput("Software"),
textOutput("c7"),
htmlOutput("SampleContent"),
textOutput("c8"),
htmlOutput("Acknowledgements"),
htmlOutput("newline2"),
downloadButton("download", "Download Checklist"),
actionButton("myToggle", "Show Examples"),
htmlOutput("newline3"),
width = 7
)
)
)
#~~~~~~~~~~~~~~~~~
# Server side
#~~~~~~~~~~~~~~~~~
scope = "Microscope"
### Reactive observe toggle Examples
server <- function(input, output, session) {
myToggle <- reactiveVal(FALSE)
observeEvent(input$myToggle, {
myToggle(!myToggle())
})
### Reactive observe Q1 WF selection to display Q1b
hide("Q1b",anim = FALSE)
hide("Q1c",anim = FALSE)
observeEvent(input$Q1, {
if(checkNull(input$Q1=="WF")){
show("Q1b", anim = TRUE)
reset("Q1b")
show("Q1c", anim=TRUE)
reset
output$cModality <- NULL
}
else if(checkNull(input$Q1)=="SConfocal"){
hide("Q1b",anim = TRUE)
show("Q1c", anim=TRUE)
reset("Q1c")
output$cModality <- renderText({
paste0(getModalityName(input$Q1),"-Specific Hardware and Settings")
})
}
else{
hide("Q1b",anim = TRUE)
hide("Q1c",anim = TRUE)
output$cModality <- renderText({
paste0(getModalityName(input$Q1),"-Specific Hardware and Settings")
})
}
})
### Title generation
output$title <- renderUI({
HTML(paste("Microscopy Metadata Checklist <br>"))
})
output$newline<- renderUI({
HTML(paste("<br>"))
})
output$newline2<- renderUI({
HTML(paste("<br>"))
})
output$newline3<- renderUI({
HTML(paste("<br> <br>"))
})
output$c1 <- renderText({
paste("Microscope Stand and Motorized Components")
})
output$c2 <- renderText({
paste("Illumination")
})
output$c3 <- renderText({
paste("Wavelength Selection")
})
output$c4 <- renderText({
paste("Optics")
})
output$c5 <- renderText({
paste("Detection")
})
output$c6 <- renderText({
paste("Acquisition Software")
})
output$c7 <- renderText({
paste("Sample Preparation")
})
output$c8 <- renderText({
paste("Acknowledgements")
})
#### Conditional checklist categories
##### Stand and Motorized Equipment
output$Stand_motorized <- renderUI({
all = ""
all <- appendChecklist(all, "all_Stand", myToggle())
if (length(input$Q4)>0 | checkNull(input$Q5)=="Y" | checkNull(input$Q6)=="Y"){
all <-appendChecklist(all, "Zstack_multiPoint_timeLapse_Stand", myToggle())
}
if ("wheel" %in% checkNull(input$Q1b) | (checkNull(input$Q1)!="no_input" & checkNull(input$Q1)!="WF")){
all <-appendChecklist(all, "emissionWheel_Stand", myToggle())
}
HTML(paste(sortItems(all)))
})
output$nonWF_Stand_motorized <- renderUI({
all = ""
if (checkNull(input$Q1)=="SConfocal") {
all <-appendChecklist(all, "Sconfocal_Stand", myToggle())
}
if (checkNull(input$Q1)=="PConfocal") {
all <-appendChecklist(all, "Pconfocal_Stand", myToggle())
}
if (checkNull(input$Q1)=="MPhoton") {
all <-appendChecklist(all, "Mphoton_Stand", myToggle())
}
HTML(paste(sortItems(all)))
})
##### Illumination
output$Illumination <- renderUI({
all = ""
if (checkNull(input$Q1)=="WF" & "LEDs" %in% checkNull(input$Q1c)) {
all <- appendChecklist(all, "WF_nolaser_Illumination", myToggle())
}
if (checkNull(input$Q1)=="WF" & "Lasers" %in% checkNull(input$Q1c)) {
all <- appendChecklist(all, "WF_laser_Illumination", myToggle())
}
if (checkNull(input$Q1)=="SConfocal" & "Lasers" %in% checkNull(input$Q1c)) {
all <- appendChecklist(all, "Sconfocal_laser_Illumination", myToggle())
}
if (checkNull(input$Q1)=="SConfocal" & "LEDs" %in% checkNull(input$Q1c)) {
all <- appendChecklist(all, "Sconfocal_LED_Illumination", myToggle())
}
if (checkNull(input$Q1)=="PConfocal") {
all <- appendChecklist(all, "Pconfocal_Illumination", myToggle())
}
if (checkNull(input$Q1)=="MPhoton") {
all <- appendChecklist(all, "Mphoton_Illumination", myToggle())
}
HTML(paste(sortItems(all)))
})
##### Wavelength Selection
output$WaveSelection <- renderUI({
all = ""
all <- appendChecklist(all, "All_Wave", myToggle())
if (checkNull(input$Q1)=="WF" & "cube" %in% checkNull(input$Q1b)) {
all <- appendChecklist(all, "WF_filterCube_Wave", myToggle())
}
HTML(paste(sortItems(all)))
})
##### Optics
output$Optics <- renderUI({
all = ""
all <- appendChecklist(all, "all_Optics", myToggle())
if (checkNull(input$Q2)=="Y") {
all <- appendChecklist(all, "transmitted_Optics", myToggle())
}
if (checkNull(input$Q3)=="Y") {
all <- appendChecklist(all, "mag_Optics", myToggle())
}
HTML(paste(sortItems(all)))
})
##### Detector
output$Detector <- renderUI({
all = ""
if (checkNull(input$Q1)=="WF") {
all <- appendChecklist(all, "WF_Detection", myToggle())
}
if (checkNull(input$Q1)=="SConfocal") {
all <- appendChecklist(all, "Sconfocal_Detection", myToggle())
}
if (checkNull(input$Q1)=="PConfocal") {
all <- appendChecklist(all, "Pconfocal_Detection", myToggle())
}
if (checkNull(input$Q1)=="MPhoton") {
all <- appendChecklist(all, "Mphoton_Detection", myToggle())
}
HTML(paste(sortItems(all)))
})
##### Software
output$Software <- renderUI({
all = ""
all <- appendChecklist(all, "all_Software", myToggle())
if (length(input$Q4)>0) {
all <- appendChecklist(all, "multiDim_Software", myToggle())
}
if ("multi-color" %in% checkNull(input$Q4)) {
all <- appendChecklist(all, "multiColor_Software", myToggle())
}
if ("z-stack" %in% checkNull(input$Q4)) {
all <- appendChecklist(all, "Z_stack_Software", myToggle())
}
if ("time-lapse" %in% checkNull(input$Q4)) {
all <- appendChecklist(all, "timeLapse_Software", myToggle())
}
if(checkNull(input$Q6)=="Y"){
all <- appendChecklist(all, "tile_Software", myToggle())
}
HTML(paste(sortItems(all)))
})
##### Sample-related
output$SampleContent <- renderUI({
all = ""
all <- appendChecklist(all, "all_Sample", myToggle())
if (checkNull(input$Q7)=="Y") {
all <- appendChecklist(all, "live_Sample", myToggle())
}
else if(checkNull(input$Q7)=="N"){
all <- appendChecklist(all, "fixed_Sample", myToggle())
}
if ("FP" %in% checkNull(input$Q8)) {
all <- appendChecklist(all, "FP_Sample", myToggle())
}
if ("Dye" %in% checkNull(input$Q8)) {
all <- appendChecklist(all, "dye_Sample", myToggle())
}
if (checkNull(input$Q9)=="Y") {
all <- appendChecklist(all, "transfect_Sample", myToggle())
}
HTML(paste(sortItems(all)))
})
##### Acknowledgements
output$Acknowledgements <- renderUI({
all = ""
if (checkNull(input$Q10)=="Y") {
all <- appendChecklist(all, "core_Ack", myToggle())
}
HTML(paste(sortItems(all)))
})
#################
# Download
################
output$download = downloadHandler(
filename = 'report.pdf',
content = function(file) {
params <- list(Metadata = Metadata,
examples= examples,
modality = getModalityName(checkNull(input$Q1)),
Q1 = checkNull(input$Q1),
Q1b = checkNull(input$Q1b),
Q1c = checkNull(input$Q1c),
Q2 = checkNull(input$Q2),
Q3 = checkNull(input$Q3),
Q4 = checkNull(input$Q4),
Q5 = checkNull(input$Q5),
Q6 = checkNull(input$Q6),
Q7 = checkNull(input$Q7),
Q8 = checkNull(input$Q8),
Q9 = checkNull(input$Q9),
Q10 = checkNull(input$Q10),
showExamples=myToggle())
src <- normalizePath('report.Rmd')
src2 <- normalizePath('checkbox.png')
# temporarily switch to the temp dir, in case you do not have write
# permission to the current working directory
owd <- setwd(tempdir())
on.exit(setwd(owd))
file.copy(src, 'report.Rmd', overwrite = TRUE)
file.copy(src2, 'checkbox.png', overwrite = TRUE)
id <- showNotification("Rendering checklist...",
duration = NULL,
closeButton = FALSE)
on.exit(removeNotification(id), add = TRUE)
library(rmarkdown)
out <- render('report.Rmd', params=params, envir = new.env()) #add , pdf_document() here if you want default latex font
file.rename(out, file)
}
)
}
shinyApp(ui = ui, server = server)