output$plot <- renderImage({
outfile <- tempfile(fileext = '.png')
png(outfile, width = 400, height = 300)
venn.diagram(
x = list(
T = T,
I = I
),
main = "Venn Diagram ",
filename =outfile, output=TRUE,
lwd = 2,na = "remove",
fill = c("orange", "blue"),
alpha = c(0.5,0.5),
label.col = "black",
cex=1.5,
fontface = "plain",
cat.col = c("cornflowerblue", "pink"),
cat.cex = 1.5,
cat.fontfamily = "serif",
cat.fontface = "plain",
cat.dist = c(0.05, 0.05),
cat.pos = c(-20, 14),
cat.default.pos = "text",
scaled = FALSE
)
dev.off()
list(src = outfile,
contentType = 'image/png',
width = 400,
height = 300,
alt = "This is alternate text")
}, deleteFile = TRUE)
I was trying plot a venn diagram using this code. But it only displays This is alternate text and not outputting any image on the app, Any Idea ?
Try to create a reactive graph as shown below
output$plot <- renderImage({
vennd <- reactive({venn.diagram(
x = list(
T = T,
I = I
),
main = "Venn Diagram ",
filename =outfile, output=TRUE,
lwd = 2,na = "remove",
fill = c("orange", "blue"),
alpha = c(0.5,0.5),
label.col = "black",
cex=1.5,
fontface = "plain",
cat.col = c("cornflowerblue", "pink"),
cat.cex = 1.5,
cat.fontfamily = "serif",
cat.fontface = "plain",
cat.dist = c(0.05, 0.05),
cat.pos = c(-20, 14),
cat.default.pos = "text",
scaled = FALSE
)
})
outfile <- tempfile(fileext = '.png')
png(outfile, width = 400, height = 300)
vennd()
dev.off()
list(src = outfile,
contentType = 'image/png',
width = 400,
height = 300,
alt = "This is alternate text")
}, deleteFile = TRUE)
output$plot <- renderImage({
vennd <- reactive({venn.diagram(
x = list(
T = T,
I = I
),
main = "",
filename =outfile, output=TRUE,
lwd = 2,na = "remove",imagetype="png",
fill = c("orange", "blue"),
alpha = c(0.5,0.5),
label.col = "black",
cex=1.5,
fontface = "plain",
cat.col = c("cornflowerblue", "pink"),
cat.cex = 1.5,
cat.fontfamily = "serif",
cat.fontface = "plain",
cat.dist = c(0.05, 0.05),
cat.pos = c(-20, 14),
cat.default.pos = "text",
scaled = FALSE
)
})
outfile <- tempfile(fileext = '.png')
png(outfile, width = 500, height = 500,type="cairo")
vennd()
dev.off()
list(src = outfile,
contentType = 'image/png',
width = 500,
height = 500,
alt = "This is alternate text")
}, deleteFile = TRUE)
Need to add imagetype="png" and type="cairo" thank you #YBS
Related
I have the code below, but the options for the individual columns widths I want to control is not doing anything.
output$search_results <- DT::renderDataTable(filtered_df(),
server=TRUE,
extensions = c('Buttons', 'ColReorder', 'FixedColumns','FixedHeader', 'KeyTable'),
options = list(
#dom = 'Blfrtip',
dom = 'Blptilp',
colReorder = TRUE,
buttons = c('copy', 'csv', 'excel'),
autoWidth = TRUE,
scrollX = TRUE,
scrollY = "500px",
fixedColumns = list(leftColumns = 2),
fixedHeader = TRUE,
keys=TRUE,
lengthMenu = c(5,10,20,50,100),
columnDefs = list(list(width = '500px', targets = c(0,1)))
)
)
I am trying to reproduce the decomposed time series plot with highchart.
The result is perfect in the working directory of r but when I put it in r shiny no result comes out.
Here is my code
library(shinyjs)
library(shiny)
library(shinydashboard)
library(highcharter)
library(forecast)
shinyOptions(bslib = TRUE)
bs_global_theme()
bs_theme_base_colors(bg = "#002B36", fg = "#EEE8D5")
bs_theme_accent_colors(primary = "#2AA198")
thematic::thematic_shiny()
ui<-fluidPage(
theme=shinytheme("cerulean"),
themeSelector(),
useShinyjs(),
navbarPage(
title= "Stock exchange", position = "static-top",
id="nav",
tabPanel("Single stock analysis",value = "single_stock", icon = icon("chart-area"),
sidebarLayout(
div(id = "Sidebar",
sidebarPanel(width = 3, align = "center",
selectInput("ticker",
strong("Ticker"),
# quotes$Symbole,
choices = c("AirPassengers", "ttrc"),
selectize = TRUE
),
dateRangeInput("date", strong("Select data range"),
start = "2012-01-01", end = (Sys.Date()-1)
),
tags$br(),
fluidPage(column(width = 3, "Session")
)
)),
mainPanel(
fluidRow(align = "center",
selectInput("hideorshow", label = strong("Sidebar disposition"),
choices = c("Show", "Hide"), selected = "Show")),
tabsetPanel(
tabPanel("Data structure and summary",
icon = icon("table"),
h1(align = "center",
strong(" STRUCTURE OF THE DATAFRAME ")),
tags$br(),tags$b(),class="fa fa-table",
verbatimTextOutput("struc"),
tags$br(),tags$br(),
h1(align = "center",strong(" SUMMARY OF THE DATAFRAME ")),
br(),verbatimTextOutput("summary1")
),
tabPanel("Dataset",icon = icon("tablet-alt"), DTOutput('tbl1')),
tabPanel("Plot",icon = shiny::icon('chart-bar'), br(),br(), br(),
airDatepickerInput(inputId = "date.ts",
strong("Time of the first observation"),
value = "2017-01-01",
minDate = "1998-09-16",
maxDate = Sys.Date(),
view = "months",
minView = "months",
dateFormat = "yyyy-mm"),
highchartOutput("closing_pr.ts",width = "auto", height = "600px"),
),
)
)
)),
tabPanel("Multiple stocks analysis", tabName = "mult_stock", icon = icon("th"))
)
)
I think the problem is hide in the server; exactely the renderHighchart but i can't find it. Please any help will be appreciate.
cs <- new.env()
dt_new <- eventReactive(c(input$ticker,input$date[1],input$date[2]), {
if (input$ticker =="AirPassengers"){
data(AirPassengers)
mydata1 <- AirPassengers
}
else if (input$ticker =="ttrc"){
data(ttrc)
mydata1 <- ttrc
}
mydata1
})
output$closing_pr.ts<-renderHighchart({
year.ts <- as.numeric(year(input$date.ts))
month.ts <- as.numeric(month(input$date.ts))
dc <- decompose(AirPassengers)
df <- as.data.frame(dc[c("x","trend","seasonal","random")])
df2 <- data.frame(Date = index(dc$x),
apply(df, 2, as.numeric))
names(df2) <- c("Date", "Observed", "Trend", "Seasonal", "Random")
df2$Date <- as.Date(yearmon(df2$Date))
df2 <- as.xts(df2[,-c(1)],
order.by = df2$Date)
df2 <- round(df2, digits = 3)
highchart(type = "stock") %>%
hc_title(text = "TIME SERIE DECOMPOSITION") %>%
hc_add_series(df2[, "Observed"], yAxis = 0, name = "Observed", showInLegend = FALSE) %>%
hc_add_yAxis(nid = 1L, title = list(text = "Observed"), relative = 2) %>%
hc_add_series(df2[, "Trend"], yAxis = 1, type = "line",name = "Trend", showInLegend = FALSE) %>%
hc_add_yAxis(nid = 2L, title = list(text = "Trend"), relative = 1)%>%
hc_add_series(df2[, "Seasonal"], yAxis = 2, type = "line",name = "Seasonal", showInLegend = FALSE) %>%
hc_add_yAxis(nid = 1L, title = list(text = "Seasonal"), relative = 2) %>%
hc_add_series(df2[, "Random"], yAxis = 3, type = "line", name = "Random", showInLegend = FALSE) %>%
hc_add_yAxis(nid = 2L, title = list(text = "Random"), relative = 1)%>%
hc_exporting(
enabled = TRUE, # always enabled,
filename = paste0("Closing price decomposition line charts from ",
min(index(df2)),
" to ", max(index(df2))))%>%
hc_colors(colors = c("blue", "red", "cyan", "darkgreen"))
})
observeEvent(input$hideorshow, {
if ( input$hideorshow== "Show") {
shinyjs::show(id = "Sidebar")}
else {shinyjs::hide(id = "Sidebar")}
})
output$summary1 <- renderPrint({
summary(dt_new())
})
output$struc<- renderPrint({
str(dt_new())
})
}
shinyApp(ui=ui, server = server)
Try this
library(shinyjs)
library(shiny)
library(shinydashboard)
library(highcharter)
library(forecast)
library(lubridate)
library(zoo)
library(xts)
shinyOptions(bslib = TRUE)
# bs_global_theme()
# bs_theme_base_colors(bg = "#002B36", fg = "#EEE8D5")
# bs_theme_accent_colors(primary = "#2AA198")
# thematic::thematic_shiny()
ui<-fluidPage(
#theme=shinytheme("cerulean"),
#themeSelector(),
useShinyjs(),
navbarPage(
title= "Stock exchange", position = "static-top",
id="nav",
tabPanel("Single stock analysis",value = "single_stock", icon = icon("chart-area"),
sidebarLayout(
div(id = "Sidebar",
sidebarPanel(width = 3, align = "center",
selectInput("ticker",
strong("Ticker"),
# quotes$Symbole,
choices = c("AirPassengers", "ttrc"),
selectize = TRUE
),
dateRangeInput("date", strong("Select data range"),
start = "2012-01-01", end = (Sys.Date()-1)
),
tags$br(),
fluidPage(column(width = 3, "Session")
)
)),
mainPanel(
fluidRow(align = "center",
selectInput("hideorshow", label = strong("Sidebar disposition"),
choices = c("Show", "Hide"), selected = "Show")),
tabsetPanel(
tabPanel("Data structure and summary",
icon = icon("table"),
h1(align = "center",
strong(" STRUCTURE OF THE DATAFRAME ")),
tags$br(),tags$b(),class="fa fa-table",
verbatimTextOutput("struc"),
tags$br(),tags$br(),
h1(align = "center",strong(" SUMMARY OF THE DATAFRAME ")),
br(),verbatimTextOutput("summary1")
),
tabPanel("Dataset",icon = icon("tablet-alt"), DTOutput('tbl1')),
tabPanel("Plot",icon = shiny::icon('chart-bar'), br(),br(), br(),
airDatepickerInput(inputId = "date.ts",
strong("Time of the first observation"),
value = "2017-01-01",
minDate = "1998-09-16",
maxDate = Sys.Date(),
view = "months",
minView = "months",
dateFormat = "yyyy-mm"),
highchartOutput("closing_prts",width = "auto", height = "600px"),
),
)
)
)),
tabPanel("Multiple stocks analysis", tabName = "mult_stock", icon = icon("th"))
)
)
server <- function(input, output, session){
cs <- new.env()
# dt_new <- eventReactive(c(input$ticker,input$date[1],input$date[2]), {
dt_new <- reactive({
if (input$ticker =="AirPassengers"){
data(AirPassengers)
print("Hello")
mydata1 <- AirPassengers
} else if (input$ticker =="ttrc"){
data(ttrc)
mydata1 <- ttrc
}
as.data.frame(mydata1)
})
df1 <- reactive({
year.ts <- as.numeric(year(input$date.ts))
month.ts <- as.numeric(month(input$date.ts))
dc <- decompose(AirPassengers)
df <- as.data.frame(dc[c("x","trend","seasonal","random")])
df2 <- data.frame(Date = index(dc$x),
apply(df, 2, as.numeric))
names(df2) <- c("Date", "Observed", "Trend", "Seasonal", "Random")
df2$Date <- as.Date(yearmon(df2$Date))
df2 <- as.xts(df2[,-c(1)],
order.by = df2$Date)
df2 <- round(df2, digits = 3)
df2
})
output$closing_prts <- renderHighchart({
df2 <- df1()
highchart(type = "stock") %>%
hc_title(text = "TIME SERIE DECOMPOSITION") %>%
hc_add_series(df2[, "Observed"], yAxis = 0, name = "Observed", showInLegend = FALSE) %>%
hc_add_yAxis(nid = 1L, title = list(text = "Observed"), relative = 2) %>%
hc_add_series(df2[, "Trend"], yAxis = 1, type = "line",name = "Trend", showInLegend = FALSE) %>%
hc_add_yAxis(nid = 2L, title = list(text = "Trend"), relative = 1)%>%
hc_add_series(df2[, "Seasonal"], yAxis = 2, type = "line",name = "Seasonal", showInLegend = FALSE) %>%
hc_add_yAxis(nid = 1L, title = list(text = "Seasonal"), relative = 2) %>%
hc_add_series(df2[, "Random"], yAxis = 3, type = "line", name = "Random", showInLegend = FALSE) %>%
hc_add_yAxis(nid = 2L, title = list(text = "Random"), relative = 1)%>%
hc_exporting(
enabled = TRUE, # always enabled,
filename = paste0("Closing price decomposition line charts from ",
min(index(df2)),
" to ", max(index(df2))))%>%
hc_colors(colors = c("blue", "red", "cyan", "darkgreen"))
})
observeEvent(input$hideorshow, {
if ( input$hideorshow== "Show") {
shinyjs::show(id = "Sidebar")}
else {shinyjs::hide(id = "Sidebar")}
})
output$tbl1 <- renderDT({datatable(dt_new())})
output$summary1 <- renderPrint({
summary(dt_new())
})
output$struc<- renderPrint({
str(dt_new())
})
}
shinyApp(ui, server)
I use DT::data.table in my shiny app, but the fixed colums can't match other cols.
It's my ui and server code:
Ui.R
DT::dataTableOutput("mytable2")
Server.R:
output$mytable2 <- DT::renderDT({
IDNAME <- soya.info$Names
names(IDNAME) <- soya.info$ID
IDNAMEsd <- IDNAME[colnames(serchSNP)[-c(1:7)]]
colnames(serchSNP)[-c(1:7)] <- paste0(colnames(serchSNP)[-c(1:7)], " (", IDNAMEsd, ")")
DT::datatable(
serchSNP,
selection = 'none', rownames = FALSE, escape = FALSE,
extensions = c("FixedColumns","Buttons"),
options = list(
buttons = list('pageLength',
list(extend = 'csv', filename = paste("snp", sep = "-")),
list(extend = 'excel', filename = paste("snp", sep = "-")),
'copy'),dom = 'Bfrtip',
pageLength = 15, columnDefs=list(list(targets="_all", class="dt-center")),
bSort = FALSE, scrollX = TRUE, fixedColumns = list(leftColumns = 6),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#676464', 'color': '#fff'});",
"}")
)
)
}, server = FALSE)
My app in https://venyao.xyz/SoybeanGDB/,
In page SNPs - Search
I am trying to convert cells in a DT:datatable into clickable buttons, which action is append a new tab on my shiny app.
I have been using this post R Shiny: Handle Action Buttons in Data Table as reference but in my case the buttons shows up like this:
My app is a bit more complicated but I will try to re-create the part that does not work
This is an shorter version of my data.frame
mut_genes <- structure(list(acc_num = c("BM0042985", "BM0393251", "BM0673028"), disease = c("Sucrase isomaltase deficiency", "Metachromatic leukodystrophy", "Fatal surfactant deficiency"), gene = c("SI", "ARSA", "ABCA3"), chrom = c("3q25.2-q26.2", "22q13.31-qter", "16p13.3"), genename = c("Sucrase-isomaltase", "arylsulfatase A", "ATP binding cassette subfamily A member 3"), gdbid = c("120377", "119007", "3770735"), omimid = c("609845", "607574", "601615"), amino = c("Leu-Pro", "Glu-Lys", "Met-Ile"), deletion = c(NA_character_, NA_character_, NA_character_), insertion = c(NA_character_, NA_character_, NA_character_), codon = c(341L, 331L, 1L), codonAff = c(341L, 331L, 1L), hgvs = c("1022T>C", "991G>A", "3G>C"), hgvsAll = c("1022TtoC | L341P", "991GtoA | E331K", "3GtoC | M1I"), dbsnp = c("rs267607049", NA, NA), chromosome = c("3", "22", "16"), startCoord = c(165060026L, 50626052L, 2326464L), endCoord = c(165060026L, 50626052L, 2326464L), inheritance = c("AR", "AR", "AR"), gnomad_AC = c(NA_integer_, NA_integer_, NA_integer_), gnomad_AF = c(NA_real_, NA_real_, NA_real_), gnomad_AN = c(NA_integer_, NA_integer_, NA_integer_), mutype = c("missense", "missense", "initiation"), pmid = c("10903344", "12809637", "16641205"), pmidAll = c(NA, NA, "24871971"), base = c("M", "M", "M"), clinvarID = c("1413", NA, NA), clinvar_clnsig = c("Pathogenic", NA, NA), gene_id = c("2073", "190", "10")), row.names = c(NA, -3L), class = c("tbl_df", "tbl", "data.frame"))
library(shiny)
library(shinyjs)
library(tidyverse)
library(DT)
sidebar <- dashboardSidebar(
selectInput("search", label = "Search Options:",
choices = c("General", "Gene", "Mutation", "Reference", "Phenotype"), selected = "Gene"),
sidebarMenu(id="siderbarmenu", sidebarMenuOutput("menu"))
)
header <- dashboardHeader()
body <- dashboardBody(
tags$style(type="text/css",
".shiny-output-error { visibility: hidden; }",
".shiny-output-error:before { visibility: hidden; }",
".shiny-output-error:after { visibility: hidden; }"),
#ui
shinyjs::useShinyjs(),
tabItems(
tabItem("search_general", h1("A was done")),
tabItem(
tabName = "search_exact_gene",
tabsetPanel(
id = "tabs",
tabPanel(
title = "Main Dashboard",
value = "gene1",
fluidRow(
column(12,dataTableOutput("tablafilt_paste_genes"))
)
)
)
)
)
)
ui <- dashboardPage(header, sidebar, body)
And Here is the server part
server <- function(input, output, session) {
output$menu <- renderMenu({
my_general = list(
menuItem("Búsqueda general", tabName="search_general"),
conditionalPanel("input.siderbarmenu == 'search_general'",
textInput(inputId = "search_terms", label = "Search terms"),
selectInput("search_fields", label="Search choices", choices=c("All Fields", "Gene symbol",
"Gene description", "Chromosomal location", "HGNC/OMIM/GDB/Entrez ID", "RefSeq transcript",
"Disease/phenotype", "Gene Ontology"), selected = "Gene symbol"),
actionButton("submit", "Submit query")
)
)
my_gene = list(
menuItem("Búsqueda por gene", tabName="search_exact_gene"),
textInput(inputId = "search_exact_symbol", label = "Exact gene symbol only"),
actionButton("submit3", "Submit query")
)
if(input$search=="General"){
menu = my_general
} else if (input$search=="Gene"){
menu = my_gene
}
sidebarMenu(menu)
})
filtrado <- reactive({
dataset <- input$submit3
glist <- isolate(input$search_exact_symbol)
datos <- filter(mut_genes, gene %in% glist)
shinyInput <- function(FUN, len, id, ...) {
inputs <- character(len)
for (i in seq_len(len)) {
inputs[i] <- as.character(FUN(paste0(id, i), ...))
}
inputs
}
datos <- mutate(datos, Mutacion=shinyInput(
FUN = actionButton,
len = nrow(datos),
id = 'button_',
label = "Mutacion",
onclick = 'Shiny.onInputChange(\"select_button\", this.id)')
)
return(datos)
})
output$tablafilt_paste_genes <- DT::renderDataTable({
if(is.null(filtrado()))
return()
datos <- filtrado()
DT::datatable(datos, escape = FALSE,
rownames = FALSE,
style = 'bootstrap',
class = 'compact cell-border stripe hover',
filter = list(position = 'top', clear = FALSE),
extensions = c('Buttons', "FixedHeader", "Scroller"),
options = list(
stateSave = FALSE,
ordering = FALSE,
autoWidth = TRUE,
search = list(regex = TRUE, caseInsensitive = TRUE),
columnDefs = list(
list(
className = 'dt-center',
targets = 1:ncol(datos)-1L,
render = JS("function(data, type, row, meta) {",
"return type === 'display' && typeof data === 'string' && data.length > 10 ?",
"'<span title=\"' + data + '\">' + data.substr(0, 10) + '...</span>' : data;",
"}")
)
),
initComplete = JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'font-size': '12px'});",
"}"),
sDom = '<"top">Brtp<"bottom">i', # remove search general box and keep the top filters
scrollX = TRUE,
deferRender=TRUE,
buttons = list('colvis'),
FixedHeader = TRUE,
pageLength = 25,
lengthMenu = list(c(25, 50, 100, -1), list('25', '50', '100', 'All'))
),
callback = JS('table.page(3).draw(false); "setTimeout(function() { table.draw(true); }, 300);"')) %>%
formatStyle(columns = colnames(.$x$data), `font-size` = "15px")
})
}
runApp(shinyApp(ui, server))
My ideal situation is recreate the acc_num column and make it a buttom clickable, but when I have tried with
shinyInput <- function(FUN, len, id, label,...) {
inputs <- character(len)
for (i in seq_len(len)) {
label <- datos$acc_num[i]
inputs[i] <- as.character(FUN(paste0(id, i), label=label, ...))
}
inputs
}
It happens the same, I still see the <button id => even when I set the datatable option escape to false
That's because of the quotes. Your render function generates <span title="<button id = "xxx" ...... and this causes the issue.
You don't want to apply the span to the buttons, so add the regex test !(/button/).test(data) in the conditions:
render = JS("function(data, type, row, meta) {",
"return type === 'display' && typeof data === 'string' && data.length > 10 && !(/button/).test(data) ? ",
"'<span title=\"' + data + '\">' + data.substr(0, 10) + '...</span>' : data;",
"}")
So I have read that using global is a bad practice. Earlier I did this entire program using just functions now I want to use classes inside the function. These are two of the functions inside the class. I am getting a function object has no attribute amountentry Error.
def addmoneyindb(self,amountentry):
#global accno
moneyentry_ip = amountentry.get()
query = "select balance from bankui where accountno ="+accno_log+""
cur.execute(query)
queryy = cur.fetchone()
amt = int(queryy[0])+int(moneyentry_ip)
amt = str(amt)
print amt
query1 = "update bankui set balance='"+amt+"' where accountno ="+accno_log+""
cur.execute(query1)
tkMessageBox.showinfo("Sucess", "Money Added Sucessfully")
db.commit()
def addmoney(self):
# global amountentry
Screen2 = Toplevel()
Screen2.title("Add Money")
Screen2.geometry("1366x768")
Screen2.configure(background = "light cyan")
Label(Screen2,text = "ADD MONEY" , height = 3, width = 155, fg = "black" , bg = "RoyalBlue" , font = ("Arial",20)).pack()
Label(Screen2,text = "" , height = 2, width = 10, fg = "black" , bg = "light cyan").pack()
Label(Screen2,text = "Enter Amount:" , height = 1, width = 20, fg = "black" , bg = "RoyalBlue" , font = ("Arial",12)).pack()
Label(Screen2,text = "" , height = 2, width = 10, fg = "black" , bg = "light cyan").pack()
amountentry = Entry(Screen2)
amountentry.pack()
Label(Screen2,text = "" , height = 2, width = 10, fg = "black" , bg = "light cyan").pack()
Button(Screen2 , text = "Submit", height =4 , width =20, fg = "black" , bg = "RoyalBlue" , command = self.addmoneyindb.amountentry.get(), font = ("Arial",12)).pack()
Label(Screen2,text = "" , height = 2, width = 10, fg = "black" , bg = "light cyan").pack()
Label(Screen2,text = "" , height = 1, width = 10, fg = "black" , bg = "light cyan").pack()
Button(Screen2 , text = "Exit", height =4 , width =20, fg = "black" , bg = "RoyalBlue" , command = Screen2.destroy , font = ("Arial",12)).pack()
Label(Screen2,text = "" , height = 1, width = 10, fg = "black" , bg = "light cyan").pack()
Screen2.mainloop()
You need to add self to the variables you want to access through other methods of the same class. Also your Button command won't work - i have modified it to print the result of self.amountentry instead.
def addmoneyindb(self): #don't need the amountentry arg
moneyentry_ip = self.amountentry.get()
...
def addmoney(self):
...
self.amountentry = Entry(Screen2)
self.amountentry.pack()
...
Button(Screen2, text="Submit", height=4, width=20, fg="black", bg="RoyalBlue",
command=lambda: print(self.amountentry.get()), font=("Arial", 12)).pack()
...