Goal: I'm working on a bioinformatics project. I'm currently trying to implement R code that dynamically creates tabPanels (they are essentially carbon copies except for the data output).
Implementation: After doing some research I implemented this solution. It works in a way (the panels that I'm "carbon copying" are created), but the data that I need cannot be displayed.
Problem: I'm sure that the way I'm displaying my data is fine. The problem is that I can't use the same output function to display the data as seen here. So let me get to the code...
ui.R
library(shiny)
library(shinythemes)
library(dict)
library(DT)
...# Irrelevant functions removed #...
geneinfo <- read.table(file = "~/App/final_gene_info.csv",
header = TRUE,
sep = ",",
na.strings = "N/A",
as.is = c(1,2,3,4,5,6,7))
ui <- navbarPage(inverse = TRUE, "GENE PROJECT",
theme = shinytheme("cerulean"),
tabPanel("Home",
#shinythemes::themeSelector(),
fluidPage(
includeHTML("home.html")
)),
tabPanel("Gene Info",
h2('Detailed Gene Information'),
DT::dataTableOutput('table')),
tabPanel("File Viewer",
sidebarLayout(
sidebarPanel(
selectizeInput(inputId = "gene", label = "Choose a Gene", choice = genes, multiple = TRUE),
selectInput(inputId = "organism", label = "Choose an Organism", choice = orgs),
selectInput(inputId = "attribute", label = "Choose an Other", choice = attributes),
width = 2),
mainPanel(
uiOutput('change_tabs'),
width = 10))),
tabPanel("Alignment")
)
I'm using uiOutput to generate tabs dynamically on the server side....
server.R
server <- function (input, output, session) {
# Generate proper files from user input
fetch_files <- function(){
python <- p('LIB', 'shinylookup.py', python=TRUE)
system(sprintf('%s %s %s', python, toString(genie), input$organism), wait = TRUE)
print('Done with Python file generation.')
# Fetch a temporary file for data output
fetch_temp <- function(){
if(input$attribute != 'Features'){
if(input$attribute != 'Annotations'){
chosen <- toString(attribute_dict[[input$attribute]])
}
else{
chosen <- toString(input$sel)
extension <<- '.anno'
}
}
else{
chosen <- toString(input$sel)
extension <<- '.feat'
}
count = 0
oneline = ''
f <- paste(toString(genie), toString(input$organism), sep = '_')
f <- paste(f, extension, sep = '')
# Writes a temporary file to display output to the UI
target <- p('_DATA', f)
d <- dict_fetch(target)
temp_file <- tempfile("temp_file", p('_DATA', ''), fileext = '.txt')
write('', file=temp_file)
vectorofchar <- strsplit(toString(d[[chosen]]), '')[[1]]
for (item in vectorofchar){
count = count + 1
oneline = paste(oneline, item, sep = '')
# Only 60 characters per line (Find a better solution)
if (count == 60){
write(toString(oneline), file=temp_file, append=TRUE)
oneline = ''
count = 0
}
}
write(toString(oneline), file=temp_file, append=TRUE)
return(temp_file)
}
# Get the tabs based on the number of genes selected in the UI
fetch_tabs <- function(Tabs, OId, s = NULL){
count = 0
# Add a select input or nothing at all based on user input
if(is.null(s)==FALSE){
selection <- select(s)
x <- selectInput(inputId = 'sel', label = "Choose an Annotation:", choices = selection$keys())
}
else
x <- ''
for(gene in input$gene){
if(count==0){myTabs = character()}
count = count + 1
genie <<- gene
fetch_files()
file_tab <- lapply(sprintf('File for %s', gene), tabPanel
fluidRow(
titlePanel(sprintf("File for %s:", gene)),
column(5,
pre(textOutput(outputId = "file")),offset = 0))
)
addTabs <- c(file_tab, lapply(sprintf('%s for %s',paste('Specific', Tabs), gene), tabPanel,
fluidRow(
x,
titlePanel(sprintf("Attribute for %s:", gene)),
column(5,
pre(textOutput(outputId = OId), offset = 0)))
))
# Append additional tabs every iteration
myTabs <- c(myTabs, addTabs)
}
return(myTabs)
}
# Select the proper file and return a dictionary for selectInput
select <- function(ext, fil=FALSE){
f <- paste(toString(genie), toString(input$organism), sep = '_')
f <- paste(f, ext, sep = '')
f <- p('_DATA', f)
if(fil==FALSE){
return(dict_fetch(f))
}
else if(fil==TRUE){
return(toString(f))
}
}
# Output gene info table
output$table <- DT::renderDataTable(
geneinfo,
filter = 'top',
escape = FALSE,
options = list(autoWidth = TRUE,
options = list(pageLength = 10),
columnDefs = list(list(width = '600px', targets = c(6))))
)
observe({
x <- geneinfo[input$table_rows_all, 2]
if (is.null(x))
x <- genes
updateSelectizeInput(session, 'gene', choices = x)
})
# Output for the File tab
output$file <- renderText({
extension <<- '.gbk'
f <- select(extension, f=TRUE)
includeText(f)
})
# Output for attributes with ony one property
output$attributes <- renderText({
extension <<- '.kv'
f <- fetch_temp()
includeText(f)
})
# Output for attributes with multiple properties (features, annotations)
output$sub <- renderText({
f <- fetch_temp()
includeText(f)
})
# Input that creates tabs and selectors for more input
output$change_tabs <- renderUI({
# Fetch all the appropriate files for output
Tabs = input$attribute
if(input$attribute == 'Annotations'){
extension <<- '.anno'
OId = 'sub'
s <- extension
}
else if(input$attribute == 'Features'){
extension <<- '.feat'
OId = 'sub'
s <- extension
}
else{
OId = 'attributes'
s <- NULL
}
myTabs <- fetch_tabs(Tabs, OId, s = s)
do.call(tabsetPanel, myTabs)
})
}
)
Explanation: Now I'm aware that there's a lot to look at here.. But my problem exists within output$change_tabs (it's the last function), which calls fetch_tabs(). Fetch tabs uses the input$gene (a list of genes via selectizeInput(multiple=TRUE)) to dynamically create a set of 2 tabs per gene selected by the user.
What's Happening: So if the user selects 2 genes then 4 tabs are created. With 5 genes 10 tabs are created... And so on and so forth... Each tab is EXACTLY THE SAME, except for the data.
Roadblocks: BUT... for each tab I'm trying to use the same output Id (since they are EXACTLY THE SAME) for the data that I want to display (textOutput(outputId = "file")). As explained above in the second link, this simply does not work because HTML.
Questions: I've tried researching several solutions, but I would rather not have to implement this solution. I don't want to have to rewrite so much code. Is there any way I can add a reactive or observer function that can wrap or fix my output$file function? Or is there a way for me to add information to my tabs after the do.call(tabsetPanel, myTabs)? Am I thinking about this the right way?
I'm aware that my code isn't commented very well so I apologize in advance. Please feel free to critique my coding style in the comments, even if you don't have a solution. Please and thank you!
