create empty dygraph in Rshiny - r

I'm using Dygraphs package for visualizing actual and the time series predicted values in R shiny. Here is the sample code that I used to generate the Dygraph. In some cases where the data points are less Holt Winters(gamma =T) does not give any prediction and I need to show an empty Dygraph with the title "Insufficient Data"). I'm not able to do this. Appreciate any help on this
library(dygraphs)
plotDyg <- fluidPage(
fluidRow(
box(selectizeInput("c1", "Enter a key",
choices = reactive({sort(unique(df$key))})(),
multiple = FALSE),width=3),
box(dygraphOutput("tsDy"), width = 10, height = 500))
)
ui <- dashboardPage(
dashboardHeader(title = "XYZ"),
dashboardSidebar(
sidebarMenu(
menuItem("abc", tabName = "sidebar2", icon = icon("bar-chart") ,
menuSubItem("def",icon = icon("folder-open"), tabName = "subMenu1")
)
)
),
dashboardBody(
tabItems(
tabItem(tabName = "subMenu1",
fluidRow(
tabBox(
title = "ghi", id = "tabset2",height = "1500px",width = 100,
tabPanel("abcdef", plotDyg)
)
)
)
)
)
)
server <- function(input, output) {
output$tsDy <- renderDygraph({
if(!is.null(input$c1)){
df.0 <- reactive({df[df$key == input$c1,]})()
tspred <- reactive({
df.0 <- convert_to_ts(df.0) # converts column "fin_var" to a monthly time series and returns the entire dataframe
act <- df.0$fin_var
hw <- tryCatch(HoltWinters(df.0$fin_var), error=function(e)NA)
if(length(hw) > 1){
p <- predict(hw, n.ahead = 12, prediction.interval = TRUE, level = 0.95)
all1 <- cbind(act, p)
}else{all1 <- matrix()}
})
if(!is.na(tspred())){
dygraph(tspred(), main = "TS Predictions") %>%
dySeries("act", label = "Actual") %>%
dySeries(c("p.lwr", "p.fit", "p.upr"), label = "Predicted") %>%
dyOptions(drawGrid = F) %>%
dyRangeSelector()
}else{dygraph(matrix(0), main = "Insufficient Data")} # I could just do 'return()' but I want to show an empty Dygraph with the title
}else{return()}
})
}

I too am unable to render Dygraphs with an empty time series. To render a message to the user I used the validate/need functions in Shiny
In your case I would replace
if(!is.na(tspred())){
With
validate(need(!is.na(tspred())), "Insufficient Data"))
This will avoid the "error: argument is of length zero" message within Dygraphs and print an appropriate message to the end user.

Related

How to filter a column in shiny whose name is an output from a slider

I have a dashboard where slider is getting updated based on a dropdown widget. My issue is that dropdown selects the name of the column, and slider filters the selected column. The issue is when i create reactive filtered dataset: specifically this line: filter(input$selectx > input$my_slider[1]. i understand that it does not work cause the input$selectx is a character name of the column (eg "mean_radius", and I need a name without quotations (eg mean_radius). I tried quote(), {{}} and other functions but could not sort it out
#loading packages
library(shiny)
library(tidyverse)
library(datateachr) #cancer_sample dataset was used from this data package
library(rstatix)
library(shinythemes)
library(shinydashboard)
ui <- dashboardPage(
dashboardHeader(title = "Cancer", titleWidth = 300),
dashboardSidebar(
width = 300,
selectInput("selectx", label = h3("Select X Variable"),
choices = list("radius_mean", "texture_mean", "perimeter_mean", "area_mean"),
selected = "area_mean"),
tags$br(),
sliderInput("my_slider",
label = h3("Range of X Variable"),
min = min(cancer_sample$area_mean, na.rm = TRUE),
max = max(cancer_sample$area_mean, na.rm = TRUE),
value = c(143.5,2501))
),
dashboardBody(
#makes the place holder for the plot
box(title = "Scatter Plot", solidHeader = TRUE, collapsible = TRUE, width = 12, plotOutput("my_plot", click = "plot_click")),
box(title = "Data Table", solidHeader = TRUE, collapsible = TRUE, width = 12, tableOutput("my_data"))
)
)
server <- function(input, output, session) {
#makes a reactive function to minimize repeated code
filtered <- reactive({
#the dataset that is being used
cancer_sample %>%
#filters the data set based on the area mean range from the slider, and the check boxes that are selected
filter(input$selectx > input$my_slider[1],
input$selectx < input$my_slider[2])
})
observe({
col <- cancer_sample %>% select(input$selectx)
#makes a slider that you can manipulate to show only data points that has an area mean that falls in the certain range
updateSliderInput(session, "my_slider",
value = col,
min = min(col, na.rm = TRUE),
max = max(col, na.rm = TRUE))
})
output$my_plot <- renderPlot({
filtered() %>%
#produces a graph with area_mean on the x-axis and perimeter_mean on the y-axis.
ggplot(aes_string(x = input$selectx, y = perimeter_mean)) +
geom_point(aes(colour = diagnosis))
})
output$my_data <- renderTable(
filtered() %>%
select(ID:area_mean)
)
}
# Run the application
shinyApp(ui = ui, server = server)
Your problem is not shiny connected, so the question could be easily simplified.
Unfortunately you do not provide the dataset here. So I could not provide a working example.
quote will always return what is inside quote(input$selectx) -> input$selectx so this for sure not a solution.
Please use the e.g. .data solution here.
airquality %>% filter(.data[[input$selectx]] > input$my_slider[1],
.data[[input$selectx]] < input$my_slider[2])

Shiny scatterplot with real-time Kaplan-Meier

I have constructed an interactive scatterplot in Shiny. Using plotly, I can select groups of points and render the annotations for this group in a table next to the plot.
library(survival)
library(survminer)
mtcars <- get(data("mtcars"))
attach(mtcars)
mtcars$OS <- sample(100, size = nrow(mtcars), replace = TRUE)
mtcars$status <- sample(0:1, size = nrow(mtcars), replace = TRUE)
library(shiny)
library(shinydashboard)
ui <- dashboardPage(
dashboardHeader(),
dashboardSidebar(
sidebarMenu(
menuItem("Test1", tabName = "test1"),
menuItem("Test2", tabName = "test2"),
menuItem("Test3", tabName = "test3"),
radioButtons("radio", h3("Choose groups"),
choices = list("Group 1" = 1, "Group 2" = 2,
"Group 3" = 3),selected = 1),
actionButton("action", "Reset")
)
),
dashboardBody(
tabItems(
tabItem(tabName = "test1",
fluidRow(
column(6,plotlyOutput("plot")),
column(width = 6, offset = 0,
DT::dataTableOutput("brush"),
tags$head(tags$style("#brush{font-size:11px;}")))
)
)
)
)
)
server <- shinyServer(function(input, output, session) {
output$plot <- renderPlotly({
key <- row.names(mtcars)
p <- ggplot(data=mtcars, aes(x=wt,y=mpg,key=key)) +
geom_point(colour="grey", size=2, alpha=1, stroke=0.5)
ggplotly(p) %>% layout(height = 500, width = 500, dragmode = "select")
})
output$brush <- DT::renderDataTable({
d <- event_data("plotly_selected")
req(d)
DT::datatable(mtcars[unlist(d$key), c("mpg", "cyl", "OS", "status")],
options = list(lengthMenu = c(5, 30, 50), pageLength = 30))
}
)
})
shinyApp(ui, server)
Example:
enter image description here
I would like to be able to select (lasso or rectangle) groups of points and display the survival curves between these groups (and p-value if possible) in a separate plot below the table. For example, the user would select 'Group1' on the menu to the left, then outline the desired groups of points, then selct 'Group 2' and select a second group of points, and so on. After each selection, the survival curves appear below the table. Once finished (and would like to restart a new comparison, the user hits 'Reset'). Here's an example output:
Example:
Expected Shiny output
I really don't know where to begin with how to incorporate this. Any help would be great, thank you
See the code below for one possible way to implement this. Throughout, rv is a reactiveValues object holding the data in a data.frame data_df. The group column in data_df tracks group membership as points are selected in the plot, and takes values of 1, 2, 3, or NA depending on whether the row is in one of the three groups. (Note: the groups are assumed to be non-overlapping.)
When the user changes the radio button selection, the plotly selection rectangle should disappear in order to prepare for the selection of the next set of points - the code below uses the shinyjs library to accomplish this, as well as to reset plotly_selected to NULL (otherwise the next rectangular selection will fail to register if it selects the same set of points as the previous one).
library(survival)
library(survminer)
library(plotly)
library(shiny)
library(shinydashboard)
library(shinyjs)
mtcars <- get(data("mtcars"))
attach(mtcars)
mtcars$OS <- sample(100, size = nrow(mtcars), replace = TRUE)
mtcars$status <- sample(0:1, size = nrow(mtcars), replace = TRUE)
jsCode <- "shinyjs.resetSel = function() { Plotly.restyle(plot, {selectedpoints: [null]});}"
ui <- dashboardPage(
dashboardHeader(),
dashboardSidebar(
sidebarMenu(
menuItem("Test1", tabName = "test1"),
menuItem("Test2", tabName = "test2"),
menuItem("Test3", tabName = "test3"),
radioButtons("radio", h3("Choose groups"),
choices = list("Group 1" = 1, "Group 2" = 2,
"Group 3" = 3), selected = 1),
actionButton("action", "Reset all Groups"),
br(),
uiOutput("currentSelections")
)
),
dashboardBody(
useShinyjs(),
extendShinyjs(text = jsCode, functions = c("resetSel")),
tabItems(
tabItem(tabName = "test1",
fluidRow(
column(6,plotlyOutput("plot")),
column(width = 6, offset = 0,
DT::dataTableOutput("brush"),
tags$head(tags$style("#brush{font-size:11px;}")))
),
fluidRow(
column(6),
column(6, plotOutput("survivalCurve"))
)
)
)
)
)
server <- shinyServer(function(input, output, session) {
## mtcars data.frame with an extra group column (initially set to NA)
rv <- reactiveValues(data_df = mtcars %>% mutate(group = NA))
## when a selection is made, assign group values to data_df based on selected radio button
observeEvent(
event_data("plotly_selected"), {
d <- event_data("plotly_selected")
## reset values for this group
rv$data_df$group <- ifelse(rv$data_df$group == input$radio, NA, rv$data_df$group)
## then re-assign values:
rv$data_df[d$key,"group"] <- input$radio
}
)
## when reset button is pressed, reset the selection rectangle
## and also reset the group column of data_df to NA
observeEvent(input$action, {
js$resetSel()
rv$data_df$group <- NA
})
## when radio button changes, reset the selection rectangle and reset plotly_selected
## (otherwise selecting the same set of points for two groups consecutively will
## not register the selection the second time)
observeEvent(input$radio, {
js$resetSel()
runjs("Shiny.setInputValue('plotly_selected-A', null);")
})
## draw the main plot
output$plot <- renderPlotly({
key <- row.names(mtcars)
p <- ggplot(data=mtcars, aes(x=wt,y=mpg,key=key)) +
geom_point(colour="grey", size=2, alpha=1, stroke=0.5)
ggplotly(p) %>% layout(height = 500, width = 500, dragmode = "select")
})
## for each group, show the number of selected points
## (not required by the rest of the app but useful for debugging)
output$currentSelections <- renderUI({
number_by_class <- summary(factor(rv$data_df$group, levels = c("1","2","3")))
tagList(
h5("Current Selections:"),
p(paste0("Group 1: ",number_by_class[1], " points selected")),
p(paste0("Group 2: ",number_by_class[2], " points selected")),
p(paste0("Group 3: ",number_by_class[3], " points selected"))
)
})
output$brush <- DT::renderDataTable({
d <- event_data("plotly_selected")
req(d)
DT::datatable(mtcars[unlist(d$key), c("mpg", "cyl", "OS", "status")],
options = list(lengthMenu = c(5, 30, 50), pageLength = 30))
})
## draw survival curves if a point has been selected
## if none have been selected then draw a blank plot with matching background color
output$survivalCurve <- renderPlot({
if (any(c(1,2,3) %in% rv$data_df$group)) {
fit <- survfit(Surv(mpg, status) ~ group,
data = rv$data_df)
ggsurvplot(fit, data = rv$data_df, risk.table = FALSE)
} else {
par(bg = "#ecf0f5")
plot.new()
}
})
})
shinyApp(ui, server)

Shiny Dashboard formatting issue

library(needs)
needs(
shiny,
ggplot2,
tidyverse,
shinydashboard,
DT
)
source("~/functions.R",local = T)
# Define UI for application that draws a histogram
header = dashboardHeader(
# tags$li(class = "dropdown",
# tags$style(".main-header {max-height: 80px}"),
# tags$style(".main-header .logo {height: 80px}")),
#title = tags$img(src='logo.png',height='100',width='200')
)
sidebar = dashboardSidebar(
menuItem("Full data",tabName="Data",icon=icon("table"),startExpanded = F,
fileInput("file","Upload CSV files",multiple=TRUE,accept=("text/comma"))),
menuItem(text = 'Simulate',tabName = 'simulate',icon=icon('chart-line'),
helpText('Simulation Parameters'),
radioButtons('type',"Please choose the type of analysis:",choices = list("Gender" = 1,"US Minority Status" = 2),selected = 1),
sliderInput("numSims","Number of simulations:",min = 1, max = 10000,step = 1000,value = 10000),
sliderInput("numYears","Number of years to simulate:",min = 1,max = 5,value = 3,step = 1),
numericInput('turnover','Total Turnover', value = 10),
sliderInput('promoRate','Set Promo rate', value = 25, min = 1, max = 100, step = 5),
sliderInput('growthRate','Set growth rate',value = 0,min=0,max=100,step = 1),
helpText('0% Growth Rate assumes a flat, constant headcount'),
actionButton('go',label = "Update"),width = 4)
)
body <- dashboardBody(
tabItems(
tabItem(
tabName = 'data',
fluidRow(wellPanel(
fileInput(
inputId = 'file',
label = "File Upload:",
accept = c("csv", ".csv")))),
wellPanel(DT::dataTableOutput('table'))),
tabItem(
tabName = 'simulate',
fluidRow(
wellPanel(
DT:::dataTableOutput('simDataTable')
))
)
))
ui = shinydashboard::dashboardPage(header,sidebar,body,skin='red')
server = server <- function(input, output) {
options(shiny.maxRequestSize = 30 * 1024 ^ 2)
dataset <- reactive({
req(input$file)
read.csv(input$file$datapath)
})
output$table = renderDataTable(dataset(), filter = 'top',options = list(scrollX = TRUE))
simulate = eventReactive(input$go,{
req(input$numSims,input$type)
x = dataset()
temp = dataSim(x,type=input$type,
numSims = input$numSims)
})
simulateAvg = reactive({
x = simulate()
y = x %>% group_by(Role) %>% summarise(mean(freq))
})
output$simDataTable = renderDataTable(simulateAvg())
}
shinyApp(ui,server)
I'm having some trouble with two issues.
1.) The formatting of the shiny dashboard is odd. The text on the side bar seems very compacted and not what other shiny dashboards look like. I'm not sure what the issue is.
2.) After upload, a table is suppose to appear on the dashboard body but it doesn't
3.) Once a table appears and I head to the simulate tab, will the dashboard body change accordingly and display the simulateAvgData set that I populated?
The dataSim function is from the source file on top. I don't receive any errors when I run anything so looking for guidance and inputs to whether or not this shiny dashboard work as intended. I'm newer to the dashboard packages from shiny.
You have a couple of issues here. You do not need a fileInput statement inside dashboardBody. Next, within dashboardSidebar, you can define fileInput at the top level of menuItem (option 1 in the code below), or a sub-level of the first menuItem (option 2 below). In either case, you need to have a menuItem with a tabName where you want to display the file that was read in. Once you read the input file, you need to select the appropriate tab to see the displayed data. Try this code
header <- dashboardHeader()
### option 1: fileInput at the first menuItem level
# sidebar <- dashboardSidebar(width=320,
# menuItem("Full data",tabName="Data",icon=icon("table"),startExpanded = F),
# fileInput("file","Upload CSV files",multiple=FALSE,accept=c("csv", ".csv"))
# )
### option 2 - fileInput as a subitem
sidebar <- dashboardSidebar(width=320,
menuItem("Full data",tabName="noData",icon=icon("table"),startExpanded = F, ## data not displayed for this tabName
menuItem("Full_data",tabName="Data", icon=icon("table")),
fileInput("file","Upload CSV files",multiple=FALSE,accept=c("csv", ".csv")))
)
body <- dashboardBody(
tabItems(
tabItem(
tabName = 'Data',
fluidRow(DTOutput('table')))
))
ui <- shinydashboard::dashboardPage(header,sidebar,body,skin='red')
server <- function(input, output, session) {
data1 <- reactive({
req(input$file)
data <- read.csv(input$file$datapath,sep = ",", header = TRUE)
})
output$table <- renderDT(data1())
}
shinyApp(ui,server)

Placing ifelse statements into a render expression Shiny

In the below code, I am attempting to create an input to show all of my markets, or just a selection within a plot and a data table. I am doing this through, or attempting, through ifelse statements within my render functions, however I am getting errors, and neither the plot or data table will render. They do render without the if else statements. I have included an Example data set to hopefully help place in context.
ui <- dashboardPage(
dashboardHeader(title = "Example"),
dashboardSidebar(
sidebarMenu(
menuItem("Dashboard", tabName = "Dashboard"),
menuItem("Example", tabName = "example"))),
dashboardBody(
tabItems(
tabItem(tabName = "Dashboard",
fluidRow(
valueBoxOutput("example"))),
tabItem(tabName = "example",
fluidRow(
box(title = "Example",
plotOutput("plotexample"), width = 12),
box(title = "Data Selection",
selectInput("market","Market(s): ", c(unique(data$marketnum),"All"),multiple = T, selectize = T, selected = "All"))),
fluidRow(
box(DT::dataTableOutput("markettable"), width = 12))))))
server <- function(input,output) {
ExampleAllMarkets <- reactive({
ExampleData %>%
group_by(Event,marketnum) %>%
summarise(ItemCount = n_distinct(ItemNumber))
})
Example <- reactive({
ExampleData %>%
filter(marketnum == input$market) %>%
group_by(Event,marketnum) %>%
summarise(PolicyCount = n_distinct(Policy_Number_9_Digit))
})
output$example <- renderValueBox({
valueBox(
paste0("44", "%"), "example", icon = icon("car"),
color = "red"
)
})
I am placing ifelse statements within my render blocks reactive to whether or not "All" is selected.
output$plotexample <- renderPlot({
ifelse(input$market=="All",
ggplot(Example(), aes(x=MBC_Number, y=ItemCount)) +
geom_bar(stat="identity"),
ggplot(ExampleAllMarkets(), aes(x=marketnum, y=ItemCount))
+
geom_bar(stat="identity"))
})
output$markettable <- DT::renderDataTable({
ifelse(input$market == "All",
ExampleAllMarkets(),
Example())
})
}
shinyApp(ui,server)
Example Data in csv format
marketnum,ItemNumber
2,118
7,101
1,109
2,109
10,101
4,102
8,100
12,103
5,106
13,116
5,112
10,103
7,113
9,114
10,112
6,114
2,116
11,113
3,107
13,102
8,107
10,109
12,110
1,120
4,106
8,116
2,112
2,106
11,101
6,108
11,107
10,111
6,120
10,118
11,119
13,117
You probably cannot use ifelse in this scenario.
Analyzing the source code for ifelse, since a plot object is not so simple, it does not just return the plot itself, but
rep(plot, length.out = 1)
or equivalently plot[1] which is just the dataset of the plot. A plot object has a length > 1 and for those, ifelse only returns its first element.
This can be easily confirmed by evaluating
> ifelse(T, c(1, 2), c(3, 4))
[1] 1
So the render function cannot draw anything, since it's input is just this dataset.
You will simply have to use the regular if else.

Display R Shiny Plot After Inputting File

I would like to display a chart (for a Shiny app), based on data inputted by a user through a file. With the current setup, there is an error message claiming the data is not found, so the plot (from the rCharts package) does not get displayed.
Code attached below:
ui.R
library(rCharts)
library(shinydashboard)
library(shiny)
dashboardPage(
skin = "black",
header <- dashboardHeader(
titleWidth = 475
),
sidebar <- dashboardSidebar(
sidebarMenu(
)
),
body <- dashboardBody(
tabItems(
tabItem("setup",
box(width = 4,title = tags$b('Input Dataset'), solidHeader = T, status = 'primary', collapsible = T,
helpText("Default max. file size is 5 MB. Please upload both files for analysis in csv format."),
fileInput("file1","Upload the first file"),
fileInput("file2","Upload the second file")
),
box(height = 500, width = 12,title = tags$b('Visualize Data'), solidHeader = T, status = 'primary',
showOutput("myPlot", "Highcharts")
)
)
)
)
)
server.R
library(shiny)
library(rCharts)
# Define server logic required to draw a histogram
shinyServer(function(input, output) {
observe({
file1 = input$file1
file2 = input$file2
if (is.null(file1) || is.null(file2)) {
return(NULL)
}
data1 = read.csv(file1$datapath)
data2 = read.csv(file2$datapath)
})
output$myPlot<-renderChart2({
# Prepare data
data1[,2] <- (data1[,2])/sum(data1[,2])
# Create chart
a <- rCharts:::Highcharts$new()
a$chart(type = "column")
a$xAxis(categories = rownames(x))
a$yAxis(title = list(text = "Normalized Intensity"))
a$data(data1)
a$set(width = 600, height = 500)
return(a)
})
})
Try adding something like this. Make sure you check for nrow and return and empty Highcharts$new() object as renderChart2 expects one.
library(shiny)
library(rCharts)
# Define server logic required to draw a histogram
shinyServer(function(input, output) {
data1 <- reactive({read.csv(file1$datapath)})
data2 <- reactive({read.csv(file2$datapath)})
output$myPlot<-renderChart2({
data1 <- data1()
# Prepare data
if(nrow(data1==0)){return(Highcharts$new())}
data1[,2] <- (data1[,2])/sum(data1[,2])
# Create chart
a <- rCharts:::Highcharts$new()
a$chart(type = "column")
a$xAxis(categories = rownames(x))
a$yAxis(title = list(text = "Normalized Intensity"))
a$data(data1)
a$set(width = 600, height = 500)
return(a)
})
})

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