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server.R
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library(shiny)
library(tibble)
library(ggplot2)
library(dplyr)
library(magrittr)
source(file = "constants.R")
source(file = "functions.R")
### Reactive Function to iterate over a variable
iterVar <- function(selected_var, tempC, buffer_IS, pH, mg, adp, atp, phosphate, seq_divisions){
iter_var <- switch(selected_var,
"tempC" = tempC,
"buffer_IS" = buffer_IS,
"pH" = pH,
"mg" = mg,
"atp" = atp,
"adp" = adp,
"phosphate" = phosphate
)
iter_range <- seq(from = iter_var[[1]],
to = iter_var[[2]],
length.out = seq_divisions)
to_plot = list()
# iterate over the range of numbers
for (x in iter_range){
# Assign the input variables based on the plotted variable (x)
iter_template <- switch(selected_var,
"tempC" = list(tempC = x,
buffer_IS = buffer_IS,
pH = pH,
mg = mg,
atp = atp,
adp = adp,
phosphate = phosphate
),
"buffer_IS" = list(tempC = tempC,
buffer_IS = x,
pH = pH,
mg = mg,
atp = atp,
adp = adp,
phosphate = phosphate
),
"pH" = list(tempC = tempC,
buffer_IS = buffer_IS,
pH = x,
mg = mg,
atp = atp,
adp = adp,
phosphate = phosphate
),
"mg" = list(tempC = tempC,
buffer_IS = buffer_IS,
pH = pH,
mg = x,
atp = atp,
adp = adp,
phosphate = phosphate
),
"atp" = list(tempC = tempC,
buffer_IS = buffer_IS,
pH = pH,
mg = mg,
atp = x,
adp = adp,
phosphate = phosphate
),
"adp" = list(tempC = tempC,
buffer_IS = buffer_IS,
pH = pH,
mg = mg,
atp = atp,
adp = x,
phosphate = phosphate
),
"phosphate" = list(tempC = tempC,
buffer_IS = buffer_IS,
pH = pH,
mg = mg,
atp = atp,
adp = adp,
phosphate = x
),
)
# get the results of the calculation
results <- calc_apparent_Keq(tempC = iter_template$tempC,
buffer_IS = iter_template$buffer_IS,
pH = iter_template$pH,
mg = iter_template$mg,
atp = iter_template$atp,
adp = iter_template$adp,
phosphate = iter_template$phosphate,
reaction = "ATP",
is0_Kref=is0_Kref_atpHyd)
# assemble the results in a list
# only selecting the apparent Gibbs energy
to_plot <- c(to_plot, results$dG_ATP)
}
# combine the results list with the variable range for plotting as a df
d <- as_tibble(list('X' = iter_range,
'j' = unlist(to_plot, recursive=FALSE)))
# calculate different unit options
# j = Joules/mol, k = Kilojoules/mol, c = kilocals/mol
d %<>% mutate(k = j/1000, cal = j*0.000239006)
return(d)
}
# server function
function(input, output, session) {
# Dynamic UI Generation
# Enable Switching plotted X variable
# By changing widget from value to range
output$tempC_output <- renderUI({
if (input$x_var == "tempC"){
val <- ui_tempC_const$default_range
} else {
val <- ui_tempC_const$default_value
}
sliderInput(inputId = "tempC",
label = h3("Temperature [°C]"),
min = ui_tempC_const$min,
max = ui_tempC_const$max,
step = ui_tempC_const$step,
value = val,
)
})
output$bufferIS_output <- renderUI({
if (input$x_var == "buffer_IS"){
val <- ui_bufferIS_const$default_range
} else {
val <- ui_bufferIS_const$default_value
}
sliderInput(inputId = "buffer_IS",
label = h3("Ionic Strength [mM]"),
min = ui_bufferIS_const$min,
max = ui_bufferIS_const$max,
step = ui_bufferIS_const$step,
value = val
)
})
output$pH_output <- renderUI({
if (input$x_var == "pH"){
val <- ui_pH_const$default_range
} else {
val <- ui_pH_const$default_value
}
sliderInput(inputId = "pH",
label = h3("pH"),
min = ui_pH_const$min,
max = ui_pH_const$max,
step = ui_pH_const$step,
value = val
)
})
output$mg_output <- renderUI({
if (input$x_var == "mg"){
val <- ui_mg_const$default_range
} else {
val <- ui_mg_const$default_value
}
sliderInput(inputId = "mg",
label = h3("Free Mg", tags$sup("2+"), "[mM]"),
min = ui_mg_const$min,
max = ui_mg_const$max,
step = ui_mg_const$step,
value = val
)
})
output$atp_output <- renderUI({
if (input$x_var == "atp"){
val <- ui_atp_const$default_range
} else {
val <- ui_atp_const$default_value
}
sliderInput(inputId = "atp",
label = h3("ATP [mM]"),
min = ui_atp_const$min,
max = ui_atp_const$max,
step = ui_atp_const$step,
value = val
)
})
output$adp_output <- renderUI({
if (input$x_var == "adp"){
val <- ui_adp_const$default_range
} else {
val <- ui_adp_const$default_value
}
sliderInput(inputId = "adp",
label = h3("ADP [mM]"),
min = ui_adp_const$min,
max = ui_adp_const$max,
step = ui_adp_const$step,
value = val
)
})
output$phosphate_output <- renderUI({
if (input$x_var == "phosphate"){
val <- ui_phosphate_const$default_range
} else {
val <- ui_phosphate_const$default_value
}
sliderInput(inputId = "phosphate",
label = h3("Phosphate [mM]"),
min = ui_phosphate_const$min,
max = ui_phosphate_const$max,
step = ui_phosphate_const$step,
value = val
)
})
# reactively cally the function to calculate the values
dataInput <- reactive({
iterVar(selected_var = input$x_var,
temp = input$tempC,
buffer_IS = input$buffer_IS,
pH = input$pH,
mg = input$mg,
adp = input$adp,
atp = input$atp,
phosphate = input$phosphate,
seq_divisions = input$num_divisions
)
})
# plot the calculated values
output$plot <- renderPlot({
# to prevent the plot from attempting to generate before
# the rest of the ui loads up
new_var <- switch(input$x_var,
"tempC" = input$tempC,
"buffer_IS" = input$buffer_IS,
"pH" = input$pH,
"mg" = input$mg,
"atp" = input$atp,
"adp" = input$adp,
"phosphate" = input$phosphate)
if (is.null(new_var) | length(new_var)==1)
return()
d <- dataInput()
x_label <- switch(input$x_var,
"tempC" = "Temperature (°C)",
"buffer_IS" = "Ionic Strength (mM)",
"pH" = "pH",
"mg" = "Free Magnesium (mM)",
"atp" = "ATP (mM)",
"adp" = "ADP (mM)",
"phosphate" = "Phosphate (mM)")
x_lim <- switch(input$x_var,
"tempC" = c(ui_tempC_const$min, ui_tempC_const$max),
"buffer_IS" = c(ui_bufferIS_const$min, ui_bufferIS_const$max),
"pH" = c(ui_pH_const$min, ui_pH_const$max),
"mg" = c(ui_mg_const$min, ui_mg_const$max),
"atp" = c(ui_atp_const$min, ui_atp_const$max),
"adp" = c(ui_adp_const$min, ui_adp_const$max),
"phosphate" = c(ui_phosphate_const$min, ui_phosphate_const$max)
)
# account for the units
anchors <- switch(input$units,
"j" = list(ymin = -63000,
ymax = -58000,
breakby=2000,
ylabel_unit = "(J/mol)"),
"k" = list(ymin = -63,
ymax = -58,
breakby=2,
ylabel_unit = "(kJ/mol)"),
"cal" = list(ymin = -15,
ymax = -13.8,
breakby=0.5,
ylabel_unit = "(kCal/mol)")
)
# Anchor ymin
if (min(d[[input$units]]) < anchors$ymin){
ymin <- round(min(d[[input$units]]) - anchors$breakby)
} else {
ymin <- anchors$ymin
}
# Anchor ymax
if (max(d[[input$units]])> anchors$ymax){
ymax <- round(max(d[[input$units]]) + anchors$breakby)
} else {
ymax <- anchors$ymax
}
p <- ggplot(d, aes(X, .data[[input$units]])) +
geom_line(size=1, color="#3F3F3F") +
geom_point(color="#3F3F3F") +
scale_x_continuous(name = x_label, limits = x_lim) +
scale_y_continuous(name = paste("Gibbs Energy", anchors$ylabel_unit),
limits = c(ymin, ymax),
breaks = seq(from=ymin,
to=ymax,
by=anchors$breakby))
print(p)
},
res=120)
}