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QuAPPro_v0-0-5.R
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QuAPPro_v0-0-5.R
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####################################
### Script Shiny R 2021 ###
### Polysome profile analysis ###
####################################
library(shiny)
library(shinythemes)
library(colourpicker)
library(stringr)
library(shinyFiles)
library(plyr)
library(colorspace)
library(markdown)
library(emg)
###################################################
### FUNCTIONS FOR APP
find_closest_minmax <- function(y, a, range)
{
d <- diff(y)
d[ d > 0 ] <- 1
d[ d < 0 ] <- -1
seg <- rle(d)
seg_ends <- cumsum(seg$lengths) # last nt of a segment
seg_starts <- c(1, seg_ends[-length(seg_ends)] + 1) # first nt of a segment
## get plateaus and their middle positions
flat <- which( seg$lengths > range & seg$values == 0 )
flat_center <- ( seg_ends[flat] + seg_starts[flat] ) / 2
up_down <- which( seg$lengths > range & seg$values != 0 )
up_down_change <- abs(diff( seg$values[up_down]) ) == 2
change_seg <- up_down[which(up_down_change) + 1]
before_change_seg <- up_down[which(up_down_change)]
minmax <- (seg_ends[before_change_seg] + seg_starts[change_seg]) / 2
all_minmax <- c(minmax, flat_center) + 0.5
closest <- order( abs(all_minmax - a), decreasing = F)[1]
return(all_minmax[closest])
}
closest_point <- function(x, y, X, Y){
all_dist <- sqrt( (x-X)^2 + (y-Y)^2)
closest <- order(all_dist, decreasing = F)[1]
return(X[closest])
}
find_closest_inflections <- function(y, a, range)
{
d <- diff(y, difference = 2)
d[ d > 0 ] <- 1
d[ d < 0 ] <- -1
seg <- rle(d)
seg_ends <- cumsum(seg$lengths) # last nt of a segment
seg_starts <- c(1, seg_ends[-length(seg_ends)] + 1) # first nt of a segment
up_down <- which( seg$lengths > range & seg$values != 0 )
up_down_change <- abs(diff( seg$values[up_down]) ) == 2
change_seg <- up_down[which(up_down_change) + 1]
before_change_seg <- up_down[which(up_down_change)]
minmax <- (seg_ends[before_change_seg] + seg_starts[change_seg]) / 2
all_minmax <- minmax + 1.5
closest <- order( abs(all_minmax - a), decreasing = F)[1]
return(all_minmax[closest])
}
smooth_profile <- function(y, spar)
{
if(is.null(spar) )
{
return( smooth.spline(1:length(y), y, spar = spar)$y )
}else{
if(spar == 0)
{
return(y)
}else{
return( smooth.spline(1:length(y), y, spar = spar)$y )
}
}
}
second_deriv <- function(y)
{
return( diff(y, differences = 2) )
}
all_min <- function(y, range)
{
d <- diff(y )
d0 <- d
d0[ d > 0 ] <- 1
d0[ d < 0 ] <- -1
seg <- rle(d0)
seg_names <- 1:length(seg$values)
seg_names <- unlist( mapply(seg_names, seg$lengths, FUN = rep) )
seg_sum <- by(d, seg_names, sum)
seg_ends <- cumsum(seg$lengths) # last nt of a segment
seg_starts <- c(1, seg_ends[-length(seg_ends)] + 1) # first nt of a segment
up_down <- which( seg$lengths >= range & seg$values != 0 )
up_down_change <- diff( seg$values[up_down]) == 2
change_seg <- up_down[which(up_down_change) + 1]
before_change_seg <- up_down[which(up_down_change)]
all_min <- 0.5 + (seg_ends[before_change_seg] + seg_starts[change_seg]) / 2
return(all_min)
}
all_max <- function(y, range)
{
d <- diff(y )
d0 <- d
d0[ d > 0 ] <- 1
d0[ d < 0 ] <- -1
seg <- rle(d0)
seg_names <- 1:length(seg$values)
seg_names <- unlist( mapply(seg_names, seg$lengths, FUN = rep) )
seg_sum <- by(d, seg_names, sum)
seg_ends <- cumsum(seg$lengths) # last nt of a segment
seg_starts <- c(1, seg_ends[-length(seg_ends)] + 1) # first nt of a segment
up_down <- which( seg$lengths >= range & seg$values != 0 )
up_down_change <- diff( seg$values[up_down]) == -2
change_seg <- up_down[which(up_down_change) + 1]
before_change_seg <- up_down[which(up_down_change)]
all_max <- 0.5 + (seg_ends[before_change_seg] + seg_starts[change_seg]) / 2
return(all_max)
}
############################
### SHINY APP:
### USER INTERFACE ###
ui <- fluidPage(
# add title for webpage tab
tags$head(tags$title("QuAPPro at MI3")),
# add shiny theme
theme = shinythemes::shinytheme(("simplex")),
#create title and subtitles visible in every tab
titlePanel(h2(tags$strong("QuAPPro"), align = "center")),
tags$h4(" - Quantification and Alignment of Polysome Profiles -", align = "center"),
#tags$hr(tags$h5(tags$strong("Load"), "your files.",tags$strong("Select"), "your profiles.",
# tags$strong("Analyze"), "using the buttons.")),
tags$head(
tags$style(
HTML(".shiny-notification {
position:fixed;
top: calc(50%);
left: calc(50%);
}
")
)
),
# create fluid layout with several tabs for displaying outputs
tabsetPanel(
# FIRST TAB
tabPanel(tags$strong("Profile Analysis"), icon = icon("chart-area"), # updated to newer version
fluidRow(column(2),
column(4, tags$h4(tags$strong("Single profiles for quantification")
)),
column(6, tags$h4(tags$strong("Multiple aligned profiles")))),
fluidRow(
column(2, style = "padding-left:20px",
# create area for uploading .pks file
fileInput("input_data", "Upload pks, txt or csv file", multiple = T, accept = c(".pks",".csv", ".txt")),
#Let user select their loaded files and set x-anchor and baseline
selectInput("select", "Select files", choices = c(), width = '100%'),
# create inputs for user to set x and y axis limits, should start with initially set values before user input
fluidRow(
column(12, tags$h4(tags$strong("Fluorescence profile")))),
fluidRow(
column(12, tags$h6("Set fluorescence baseline"))),
fluidRow(
# show fluorescence signal or not?
# set a separate baseline for the fluorescence signal
column(6, style = "padding-top:10px",actionButton("baseline_fl", "Baseline", width = '100%')
),
column(6,style = "padding-top:8px",
checkboxInput("show_fl", "Show fluorescence signal", value = FALSE, width = NULL))
),
fluidRow(
column(6, style = "padding-top:10px",
numericInput("axis1_fl", "Set y min", value = NULL, step = 1)
),
column(6, style = "padding-top:10px",
numericInput("axis2_fl", "Set y max", value = NULL, step = 1))),
# introduce a slider for smoothing of the fluorescence signal
column(12,
fluidRow(sliderInput("slider1", label = "Smooth fluorescence profile", min = 0,
max = 1, value = 0, step = 0.01)))
),
column(4, style = "padding-top:22px",
plotOutput("plot_single", click = "click")
),
column(4, style = "padding-top:22px",
plotOutput("plot_align")
),
column(2, style = "padding-right:22px",
# create inputs for user to set x and y axis limits, should start with initially set values before user input
fluidRow(tags$h5(tags$strong("Fluorescence profile")),
# show fluorescence signal or not?
column(12,
checkboxInput("show_fl_al", "Show fluorescence signal", value = FALSE, width = NULL)
),
column(6,
numericInput("axis1_a_fl", "Set y min", value = NULL, step = 1)),
column(6,
numericInput("axis2_a_fl", "Set y max", value = NULL, step = 1))
),
fluidRow(tags$h5(tags$strong("Polysome profile")),
column(6,
numericInput("axis1_a", "Set y min", value = NULL, step = 1)),
column(6,
numericInput("axis2_a", "Set y max", value = NULL, step = 1))
),
fluidRow(
column(6,
numericInput("axis3_a", "Set x min", value = NULL, step = 1)
),
column(6,
numericInput("axis4_a", "Set x max", value = NULL, step = 1)
)
)
)
),
fluidRow(
column(4, style = "padding-left:20px",
fluidRow(
column(6,
tags$h4(tags$strong("Polysome profile"))
),
column(6,
tags$h4(tags$strong("Quantification"))
)
),
fluidRow(
column(6,
tags$h6("Set baseline and alignment anchor")
),
column(6,
tags$h6("Set area start and end")
)
),
fluidRow(
column(3,style = "padding-top:10px", actionButton("baseline", "Baseline", width = '100%'
)
),
column(3,style = "padding-top:10px", actionButton("x_anchor", "X-anchor", width = '100%')
),
column(3, style = "padding-top:10px",
actionButton("file_start", "Start", width = '100%')
),
column(3, style = "padding-top:10px",
actionButton("file_end", "End", width = '100%')
)
),
fluidRow(
column(3, style = "padding-top:10px",
numericInput("axis1", "Set y min", value = NULL, step = 1)
),
column(3, style = "padding-top:10px",
numericInput("axis2", "Set y max", value = NULL, step = 1)
),
column(3, style = "padding-top:10px",
selectInput("select_area", "Select area to quantify", choices = c("Total", "Monosomes", "Polysomes", "40S", "60S"), width = '100%')
),
column(3, style = "padding-top:10px",
textInput("name_area", "Optional: Name area", value = "", width = NULL, placeholder = "Unknown peak")
)
),
fluidRow(
column(3, style = "padding-top:0px",
numericInput("axis3", "Set x min", value = NULL, step = 1)
),
column(3, style = "padding-top:0px",
numericInput("axis4", "Set x max", value = NULL, step = 1)
),
column(3, style = "padding-top:22px",
actionButton("quantify_area", "Quantify", width = '100%')
),
column(3, style = "padding-top:22px",
actionButton("take_over_name", "Add name", width = '100%')
)
),
fluidRow(
column(6,
checkboxInput("red_lines", "Show baseline and x-anchor", value = TRUE, width = NULL)
),
column(6,
checkboxInput("green_lines", "Show area and lines", value = TRUE, width = NULL)
)
)
),
column(2,
fluidRow(
downloadButton("downloadSinglePlot", "Download plot", icon = icon("file-download"), width = '100%')
),
fluidRow(
radioButtons("helper_functions", "Use helper functions for setting vertical lines:",
c("Help find min/max" = "peak_help",
"Help find inflections" = "inflection_help",
"No usage of helper functions" = "no_help"), selected = "peak_help"),
style = "padding-top:20px"
),
style = "padding-left:35px"
),
column(2,
# let user select files ready to align
fluidRow(
column(12,
tags$h4(tags$strong("Alignment"))
)
),
fluidRow(
column(12,
tags$h6("(Baseline and x-anchor need to be set)")
)
),
fluidRow(
column(8,
selectInput("select_alignment", "Available profiles", choices = c(), width = '100%')
),
column(1, style = "padding-top:20px",
actionButton("up", label = NULL, icon = icon("angle-double-up"), width = '100%',
style = "padding-left:5px"
)
),
column(1, style = "padding-top:20px",
actionButton("down", label = NULL, icon = icon("angle-double-down"), width = '100%',
style = "padding-left:5px"
)
),
column(2)
),
fluidRow(
column(12,
tags$h6("Remove and restore profiles from alignment"))
),
fluidRow(
column(6,
actionButton("remove_file", "Hide", icon = icon("trash"), width = '100%')
),
column(6,
actionButton("add_file", "Show", icon = icon("trash-restore"), width = '100%')
),
style = "padding-right:35px"
)
),
column(2, #changing their color and linetype seing the changes directly in the plot
fluidRow(
radioButtons("color_palette", "Select default color palette:",
c("Dark palette" = "dark_palette",
"Rainbow palette" = "rainbow_palette",
"Color blind friendly palette" = "color_blind"
), selected = "dark_palette"),
style = "padding-top:20px"
),
fluidRow(
tags$h6("Adjust selected profile yourself:")
),
fluidRow(
column(5,
colourInput("color", "Colors", palette = "square", value = "#FFFFFF")
),
column(4, style = "padding-left:0px",
selectInput("linetype", "Type", choices = c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash"),
selected = "solid")
),
column(3, style = "padding-left:0px",
numericInput("linewidth", "Width", value = 1, min = 0)
)
)
),
column(2,
downloadButton("downloadPlot", "Download plot", icon = icon("file-download"), width = '100%'),
checkboxInput("anchor_line", "Display x-anchor in alignment", value = TRUE, width = NULL),
checkboxInput("normalize_height", HTML("Normalize <b>height</b> in alignment <br/> (Requirement: ALL total areas)"), value = FALSE, width = NULL),
checkboxInput("normalize_length", HTML("Normalize <b>length</b> in alignment <br/> (Requirement: ALL total areas)"), value = FALSE, width = NULL))
)
),
# SECOND TAB
# for user-guided peak-deconvolution
tabPanel(tags$strong("Deconvolution"), icon = icon("cut"),
fluidRow(column(2),
column(4, tags$h4(tags$strong("Single profile for deconvolution"))
),
column(6)
),
fluidRow(
column(2, style = "padding-left:20px",
#Let user select their loaded files and set x-anchor and baseline
selectInput("select2", "Select files", choices = c(), width = '100%'),
# create inputs for user to set x and y axis limits, should start with initially set values before user input
fluidRow(
column(12, tags$h4(tags$strong("Identify peaks")))),
fluidRow(
column(12, style = "padding-left:20px",
tags$h5(tags$strong("Peaks can be identified from local maxima with different resolution:")))
),
column(12,
fluidRow(sliderInput("slider3",
label = "Resolution",
min = 50,
max = 100, value = 95)
)
),
fluidRow(
column(12, style = "padding-left:20px",
tags$h5(tags$strong("Hidden peaks can be identified from 2nd deriv. minima after smoothing.")))
),
# introduce a slider for smoothing of the fluorescence signal
column(12,
fluidRow(sliderInput("slider2",
label = "Smoothing",
min = 0,
max = 1, value = 0.3, step = 0.01))),
fluidRow(
column(6,
checkboxInput("show_deriv", "Show 2nd deriv. minima", value = FALSE, width = NULL)
),
column(6,
checkboxInput("show_local_max", "Show local maxima", value = TRUE, width = NULL)
)
),
fluidRow(
column(12, style = "padding-left:20px",
tags$h4(tags$strong("Deconvolution"))
)
),
fluidRow(
column(12, style = "padding-left:20px",
tags$h5(tags$strong("Select or add peaks by clicking into the plot."))
)
),
fluidRow(
column(6, style = "padding-top:10px",
numericInput("height", "Height", value = NULL, step = 0.5)
),
column(6, style = "padding-top:10px",
numericInput("SD", "Width", value = 0.1, min = 0.01, step = 0.01)
)
),
fluidRow(
column(12, sliderInput(
"slider4", label = "Degree of asymmetry", value = 0, min = -0.2, max = 0.2,
step = 0.01)
)
),
fluidRow(
column(12,style = "padding-top:32px", actionButton("delete_peak", "Delete peak", width = '100%',
icon = icon("trash"))
)
)
),
column(8, style = "padding-top:22px",
textOutput("test"),
plotOutput("plot_deconv", click = "click_deconv", height = 700)
),
column(2, style = "padding-right:22px",
# create inputs for user to set x and y axis limits, should start with initially set values before user input
fluidRow(tags$h4(tags$strong("Axis limits")),
column(6,
numericInput("axis1_d", "Set y min", value = NULL)),
column(6,
numericInput("axis2_d", "Set y max", value = NULL))
),
fluidRow(
column(6,
numericInput("axis3_d", "Set x min", value = NULL)),
column(6,
numericInput("axis4_d", "Set x max", value = NULL))
),
fluidRow(
column(12,
tags$h4(tags$strong("Peak quantification"))
)
),
fluidRow(
column(6, style = "padding-top:10px",
selectInput("select_peak", "Peak to quantify", choices = c("40S", "60S", "Monosomes", "Halfmers"), width = '100%')
),
column(6, style = "padding-top:10px",
textInput("name_peak", "Optional: Name peak", value = "", width = NULL, placeholder = "Unknown peak")
)
),
fluidRow(
column(6, style = "padding-top:10px",
actionButton("quantify_peaks", "Quantify", width = '100%')
),
column(6, style = "padding-top:10px",
actionButton("take_over_peak", "Add name", width = '100%')
)
),
fluidRow(
column(6,
downloadButton("downloadDeconv", "Download plot", icon = icon("file-download"), width = '100%')
),
column(6),
style = "padding-top:22px"
)
)
)
),
# THIRD TAB
# shows updating table of quantified areas for respective plots, download possible
tabPanel(tags$strong("Quantification summary"), icon = icon("list-alt"),
column(6,
tags$h4("Table of quantified areas"),
tableOutput("quantification"),
downloadButton("downloadQuant", "Download .csv file")
),
column(6,
tags$h4("Table of quantified peaks"),
tableOutput("quantification_peaks"),
downloadButton("downloadQuant_peaks", "Download .csv file")
)
),
# FOURTH TAB
# shows updating table of aligned (and normalized) profiles, download possible
tabPanel(tags$strong("Alignment table"), icon = icon("table"),
tags$h4("Table of all aligned (and normalized) profiles"),
downloadButton("downloadData", "Download .csv file"),
tableOutput("csv_file")),
# FIFTH TAB
# shows Rmd manual
tabPanel(tags$strong("QuAPPro manual"), icon = icon("question-circle"),
fluidRow(
column(2),
column(8, htmltools::includeMarkdown("RMD_menu_template_2022.Rmd")),
column(2))
),
# SIXTH TAB
# general information and impressum
tabPanel(tags$strong("Release notes", style = "color:blue"), icon = icon("info", style = "color:blue"),
tags$h4("Release notes"),
tags$div("This is version QuAPPro v0.0.5.
To run it locally, you can download the code from our GitHub repository:",
tags$a(href="https://github.com/johannaschott/QuAPPro", "https://github.com/johannaschott/QuAPPro", style = "color:blue")
)
),
# SEVENTH TAB
# general information and impressum
tabPanel(tags$strong("Contact", style = "color:blue"), icon = icon("address-card", style = "color:blue"),
tags$h4("About Us"),
tags$div("This shiny app was developed by Chiara Schiller and",
tags$a(href="https://www.umm.uni-heidelberg.de/biochemie/research/research-johanna-schott/", "Johanna Schott", style = "color:blue"),
"at the",
tags$a(href="https://www.umm.uni-heidelberg.de/medical-faculty-mannheim/home/", "Medical Faculty Mannheim", style = "color:blue"),
"(",
tags$a(href="https://www.umm.uni-heidelberg.de/mi3/", "MI3", style = "color:blue"),
",",
tags$a(href="https://www.umm.uni-heidelberg.de/biochemie/", "Stoecklin lab", style = "color:blue"),
")."
),
tags$h4("Acknowledgements"),
tags$div("We would like to thank Dr. Andreas Bohne-Lang at the",
tags$a(href="https://www.umm.uni-heidelberg.de/fakultaet/edv/", "IT department", style = "color:blue"),
"of the Medical Faculty Mannheim and all members of the Stoecklin lab for support and input."),
tags$h4(tags$a(href="https://www.umm.uni-heidelberg.de/impressum/", "Impressum", style = "color:blue") )
)
))
#### SERVER ####
server <- function(input, output, session) {
### REACTIVE VALUES FOR LISTS BUILT ALONG THE SESSION
# create reactive values for collecting values in a list/vector/data.frame
val <- reactiveValues(
paths_collected = vector()
)
val <- reactiveValues(
colors_collected = list()
)
val <- reactiveValues(
color_vector = vector()
)
val <- reactiveValues(
linetype_collected = list()
)
val <- reactiveValues(
linewidth_collected = list()
)
val <- reactiveValues(
file_starts = list()
)
val <- reactiveValues(
file_ends = list()
)
val <- reactiveValues(
sum_areas = list()
)
val <- reactiveValues(
sum_additive_areas = list()
)
val <- reactiveValues(
file_starts_add = list()
)
val <- reactiveValues(
file_ends_add = list()
)
val <- reactiveValues(
files_to_align = vector()
)
val <- reactiveValues(
files_to_plot = vector()
)
val <- reactiveValues(
remove_files_list = vector()
)
val <- reactiveValues(
csv_file_df = data.frame()
)
val <- reactiveValues(
df_quant = data.frame()
)
val <- reactiveValues(
factors_list = list()
)
val <- reactiveValues(
control_baseline = list()
)
val <- reactiveValues(
fl_control_baseline = list()
)
val <- reactiveValues(
file_types = vector()
)
val <- reactiveValues(
xmin_collected = list()
)
val <- reactiveValues(
xmax_collected = list()
)
val <- reactiveValues(
ymin_collected = list()
)
val <- reactiveValues(
ymax_collected = list()
)
val <- reactiveValues(
ymin_collected_fl = list()
)
val <- reactiveValues(
ymax_collected_fl = list()
)
### INITIAL LOADED FILES
# update select output field with the name of every newly loaded file
observe({
session$userData$files_list <- c(input$input_data$name[input$input_data$size != 0], session$userData$files_list)
updateSelectInput(session, "select",
choices = session$userData$files_list)
})
# notification if empty file is loaded
observeEvent(input$input_data,{
if(length(input$input_data$name[input$input_data$size != 0]) != length(input$input_data$name)){
if((length(input$input_data$name) - length(input$input_data$name[input$input_data$size != 0])) == 1)
{showNotification(paste0("File ",input$input_data$name[input$input_data$size == 0]," is empty and will be ignored."),
duration = NULL, type = "message")
}else if((length(input$input_data$name) - length(input$input_data$name[input$input_data$size != 0])) > 1){
showNotification(paste0("Files ",paste(input$input_data$name[input$input_data$size == 0], collapse = ", ")," are empty and will be ignored."),
duration = NULL, type = "message")}
}
})
observe({
req(input$select)
if((grepl(".pks",as.character(input$select)) == T)){
val$factors_list[[input$select]] <- (0.1/60)
val$file_types[input$select] <- "pks"
}else if((grepl(".csv",as.character(input$select)) == T) & ("SampleFluor" %in% colnames(file_plot()))){
val$factors_list[[input$select]] <- (0.32/60)
val$file_types[input$select] <- "csv_fluo"
}else if((grepl(".csv",as.character(input$select)) == T) & !("SampleFluor" %in% colnames(file_plot()))){
val$factors_list[[input$select]] <- (0.2/60)
val$file_types[input$select] <- "csv"
print(val$factors_list[[input$select]])
}else if((grepl(".txt",as.character(input$select)) == T)){
val$factors_list[[input$select]] <- (0.1/60)
val$file_types[input$select] <- "pks"
}
})
# when an input file is selected store the path to the selected file name as current_path
current_path <- reactive({
val$paths_collected[input$input_data$name] <- input$input_data$datapath
val$paths_collected[input$select]
})
# read selected datapath from the current selected file (input$select) for input data storage
file_plot <- reactive({
#require that the input is available
req(input$select)
if(grepl(".pks",as.character(input$select)) == T){
read.table(current_path(), dec = ",", header = F)
}else if(grepl(".csv",as.character(input$select)) == T){
start <- grep("Data Columns:", readLines(current_path()))
read.csv(current_path(), skip = start)
}else if(grepl(".txt",as.character(input$select)) == T){
read.delim(current_path())}
})
# Setting y and x column values for plotting from the loaded dataset
yvalue <- reactive({
req(input$select)
if((grepl(".pks",as.character(input$select)) == T)){
file_plot()[ ,3]}else if((grepl(".csv",as.character(input$select)) == T) & ("SampleFluor" %in% colnames(file_plot()))){
file_plot()[ ,5]}else if((grepl(".csv",as.character(input$select)) == T) & (ncol(file_plot()) == 4)){
head(file_plot()[,2], -1)
}else if((grepl(".txt",as.character(input$select)) == T)){
file_plot()[ ,2]
}
})
fluorescence <- reactive({
req(input$select)
req(input$show_fl)
if((grepl(".csv",as.character(input$select)) == T) & ("SampleFluor" %in% colnames(file_plot()))){
smooth_profile( file_plot()[ ,3], input$slider1 )}
})
xvalue <- reactive({
req(input$select)
if(grepl(".pks",as.character(input$select)) == T){
(file_plot()[ ,1]+1)*val$factors_list[[input$select]]}else if((grepl(".csv",as.character(input$select)) == T) & ("SampleFluor" %in% colnames(file_plot()))){
(1:length((file_plot()[ ,4])))*val$factors_list[[input$select]]
}else if((grepl(".csv",as.character(input$select)) == T) & !("SampleFluor" %in% colnames(file_plot()))){
(head(1:length(file_plot()[,1]),-1))*val$factors_list[[input$select]]
}else if((grepl(".txt",as.character(input$select)) == T)){
(file_plot()[ ,1]+1)*val$factors_list[[input$select]]
}
})
# Create axis limits for plot area, starting with 0 and max limit values of the plotted dataset
# axis labels are modified if there are more than three numerals
lost_num_fl <- reactive({
max_numeral <- max( floor(log10(abs( fluorescence() ))) + 1 ) # how many numerals has the maximum UV absorption?
if(max_numeral > 2 ){
10^(max_numeral - 2)
}else{
1
}
})
lost_num_pol <- reactive({
max_numeral <- max( floor(log10(abs( yvalue() ))) + 1 ) # how many numerals has the maximum UV absorption?
if(max_numeral > 2 ){
10^(max_numeral - 2)
}else{
1
}
})
# When user selects other axis limits, limit values change
ymin_single <- reactive({
if(isTruthy(val$ymin_collected[[input$select]])){
val$ymin_collected[[input$select]]*lost_num_pol()
}else{
0
}})
ymin_single_fl <- reactive({
if(isTruthy(val$ymin_collected_fl[[input$select]])){
val$ymin_collected_fl[[input$select]]*lost_num_fl()
}else{
0
}})
ymax_single <- reactive({
if(isTruthy(val$ymax_collected[[input$select]])){
val$ymax_collected[[input$select]]*lost_num_pol()
}else{
max(yvalue())
}})
ymax_single_fl <- reactive({
if(isTruthy(val$ymax_collected_fl[[input$select]])){
val$ymax_collected_fl[[input$select]]*lost_num_fl()
}else{
max(fluorescence())
}})
xmin_single <- reactive({
req(input$select)
if(isTruthy(val$xmin_collected[[input$select]])){
val$xmin_collected[[input$select]]
}else{
0
}})
xmax_single <- reactive({
if(isTruthy(val$xmax_collected[[input$select]])){
val$xmax_collected[[input$select]]
}else{
max(xvalue())
}})
#### ALIGNMENT:
# value of val$buttons changes by clicking on different action buttons triggering the respective action(s).
# initial value of val$buttons and value after selecting a new file is reset to 10 (value 10 not used and also not NA)
val <- reactiveValues(
buttons = 10)
observeEvent(input$select,{
val$buttons = 10
})
# specific values set for val$buttons after clicking on specific buttons
observeEvent(input$x_anchor, {val$buttons = 1})
observeEvent(input$baseline, {val$buttons = 2})
observeEvent(input$align, {val$buttons = 3})
observeEvent(input$file_start, {val$buttons = 4})
observeEvent(input$file_end, {val$buttons = 5})
observeEvent(input$baseline_fl, {val$buttons = 6})
# setting profile start and end, x-anchor and baseline triggered by clicking into the plot.
# Values get stored as list or vector
# Either function for helping to find max and min is used or not (tick box input$peak_help)
observeEvent(input$click$x, {
# only runs when button was pressed
req(val$buttons)
# setting profile start
if(val$buttons == 4)
if(input$helper_functions == "peak_help"){
val$file_starts[[input$select]] <- (find_closest_minmax(smooth_profile(yvalue(), NULL),
(closest_point(input$click$x,
input$click$y,
xvalue(),
yvalue()))/val$factors_list[[input$select]], 5))
}else if(input$helper_functions == "inflection_help"){
val$file_starts[[input$select]] <- (find_closest_inflections(smooth_profile(yvalue(), NULL),
(closest_point(input$click$x,
input$click$y,
xvalue(),
yvalue()))/val$factors_list[[input$select]], 5))
}else{
val$file_starts[[input$select]] <-(closest_point(input$click$x,
input$click$y,
xvalue(),
yvalue())/val$factors_list[[input$select]])
}
# setting profile ends
if(val$buttons == 5)
if(input$helper_functions == "peak_help"){
val$file_ends[[input$select]] <- (find_closest_minmax(smooth_profile(yvalue(), NULL),
(closest_point(input$click$x,
input$click$y,
xvalue(),
yvalue()))/val$factors_list[[input$select]], 5))
}else if(input$helper_functions == "inflection_help"){
val$file_ends[[input$select]] <- (find_closest_inflections(smooth_profile(yvalue(), NULL),
(closest_point(input$click$x,
input$click$y,
xvalue(),
yvalue()))/val$factors_list[[input$select]], 5))
}else{
val$file_ends[[input$select]] <-(closest_point(input$click$x,
input$click$y,
xvalue(),
yvalue())/val$factors_list[[input$select]])
}
# setting baseline for polysome profile
if(val$buttons == 2){
val$baseline[input$select] <- yvalue()[(input$click$x)/val$factors_list[[input$select]]]
}
# setting baseline for fluorescence profile
if(val$buttons == 6){
par(xpd = T)
val$baseline_fl[input$select] <- fluorescence()[(input$click$x)/val$factors_list[[input$select]]]
}
# setting x-anchor
if(val$buttons == 1)
if(input$helper_functions == "peak_help"){
val$anchor[input$select] <- round(find_closest_minmax(smooth_profile(yvalue(), NULL),
(closest_point(input$click$x,
input$click$y,
xvalue(),
yvalue()))/val$factors_list[[input$select]], 5))
}else if(input$helper_functions == "inflection_help"){
val$anchor[input$select] <- (find_closest_inflections(smooth_profile(yvalue(), NULL),
(closest_point(input$click$x,
input$click$y,
xvalue(),
yvalue()))/val$factors_list[[input$select]], 5))
}else{
val$anchor[input$select] <-(closest_point(input$click$x,
input$click$y,
xvalue(),
yvalue())/val$factors_list[[input$select]])
}
# if both, anchor and baseline, exist for one plot, select_alignment button gets updated with this file
session$userData$align_files_list <- c((intersect(names(val$baseline),
names(val$anchor))),
session$userData$align_files_list)
updateSelectInput(session, "select_alignment",
choices = session$userData$align_files_list)
# reactive vector with respective file names gets updated
val$files_to_align <- intersect(names(val$baseline), names(val$anchor))
})
# update choices of areas to be quantified with names given by the user
observeEvent(input$take_over_name,{
session$userData$area_list <- c(input$name_area, session$userData$area_list)
updateSelectInput(session, "select_area",
choices = c(session$userData$area_list, "Total", "Monosomes", "Polysomes", "40S", "60S"))
})
# show notification if one of the 3 required values is missing for area quantification, but quantify button is pressed
observeEvent(input$quantify_area,{
# only execute when all required values are set
if(is.null(val$file_starts[[input$select]])|is.null(val$file_ends[[input$select]])|is.null(val$baseline[input$select])){
showNotification(paste("Please be sure to have set start, end and baseline of the area."),
duration = NULL, type = "message")
}
})