Save features created with leaflet.draw to comptuer - draw

I am working on a leaflet map and I want to use leaflet.draw plugin to provide the option to the user to draw vector and markers. Next, I would like to offer the option to the user to save the vectors/markers to their computer (e.g., as geojson). I am looking for pointers and examples how to implement this.

If you can get all the features into a LayerGroup, then you could call toGeoJSON() on it - see http://leafletjs.com/reference.html#layergroup-togeojson. The results of that could then be given to FileSaver.js for a client-side download, like
var blob = new Blob([JSON.stringify(result)], {type: "application/json;charset=utf-8"});
saveAs(blob, "features.json");

editCoord <- function(){
pgn <- NULL
if(length(input$map_draw_all_features$features) != 0) {
if(unique(unlist(lapply(input$map_draw_all_features$features, function(x){x$geometry$type}))) == "Polygon") {
for(j in 1:length(input$map_draw_all_features$features)){
geo <- unlist(lapply(input$map_draw_all_features$features[j], function(x){x$geometry$coordinates}))
v <- seq(1, length(geo), 2)
n <- length(geo)/2
for (i in 1:n) {
xy <- c(geo[v[i]], geo[i*2])
if (i == n) break()
pgn <- c(pgn, paste0(xy[1]," ",xy[2],","))
}
pgn <- c(pgn, paste0(xy[1]," ",xy[2]))
}
cat(pgn, "\n", file=paste0("f", input$usertext))
readLines(paste0("f", input$usertext))
}
}
}
editPlot <- function(){
db <- dbConnect(MySQL(), dbname = "watsan", host = options()$rds$host,
port = options()$rds$port, user = options()$rds$user,
password = options()$rds$password)
# Construct the update query
query <- paste0('UPDATE plots SET `geom_plot`= ST_GeomFromText("POLYGON((',"",Coord(),"",'))") WHERE `parcel_id`=',"'", ID() ,"'",';')
query <- gsub('\"', "'", query)
# Submit the fetch query and disconnect
dbGetQuery(db, query)
dbDisconnect(db)
}

Related

Shiny - assigning argument to function

I am trying to create a shiny app that applies a self-made function to an uploaded dataset, then allows to download the modified results. Here is my code:
library(shiny)
library(tidyverse)
namkurz <- function(data, a_spalte) {
kuerzel <- vector(length = length(data$a_spalte))
for (i in 1:length(data$a_spalte)){
spez = data$Art[i]
s = unlist(strsplit(spez, " ", fixed = TRUE))
s = substr(s, 1, 2)
s = paste(s, collapse = ' ')
kuerzel[[i]] = s
}
data <- data %>%
mutate(kurz = kuerzel)
}
ui <- fluidPage(
fileInput('upload','Deine Kartierungsdaten'),
textInput('art', 'Wie heißt die Spalte mit Artnamen?'),
downloadButton('analyse','Artenkürzel hinzufügen')
)
server <- function(input, output, session) {
data <- reactive({
req(input$upload)
ext <- tools::file_ext(input$upload$name)
switch(ext,
csv = vroom::vroom(input$upload$datapath, delim = ";"),
validate("Invalid file; Please upload a .csv file")
)
})
art <- reactive(input$art)
output$analyse <- downloadHandler(
filename = function() {
paste0('mit_kuerzel', ".csv")
},
content = function(file) {
ergebnis <- reactive(namkurz(data(), art()))
vroom::vroom_write(ergebnis(), file)
}
)
}
shinyApp(ui, server)
When trying to save the output I get a 'Warning: Unknown or uninitialised column:' error. I think my problem is in the assignment of argument 'art' to the 'ergebnis' object, but I can't find the way to fix it.
I recommend a few things:
(Required) In your function, a_spalte is a character vector and not the literal name of column in the frame, so you need to use [[ instead of $, see The difference between bracket [ ] and double bracket [[ ]] for accessing the elements of a list or dataframe and Dynamically select data frame columns using $ and a character value.
Change all references of data$a_spalte to data[[a_spalte]].
namkurz <- function(data, a_spalte) {
kuerzel <- vector(length = length(data[[a_spalte]]))
for (i in 1:length(data[[a_spalte]])){
spez = data$Art[i]
s = unlist(strsplit(spez, " ", fixed = TRUE))
s = substr(s, 1, 2)
s = paste(s, collapse = ' ')
kuerzel[[i]] = s
}
data <- data %>%
mutate(kurz = kuerzel)
}
Your function is a bit inefficient doing things row-wise, we can vectorize that operation.
namkurz <- function(data, a_spalte) {
spez <- strsplit(data$Art, " ", fixed = TRUE)
data$kurz <- sapply(spez, function(z) paste(substr(z, 1, 2), collapse = " "))
data
}
(Optional) The content= portion of downloadHandler is already reactive, you do not need to wrap namkurz in reactive. Because of this, you also don't need to treat ergebnis as reactive.
output$analyse <- downloadHandler(
filename = ...,
content = function(file) {
ergebnis <- namkurz(data(), art())
vroom::vroom_write(ergebnis, file)
}
)
(Optional) Your output filename is fixed, so two things here: if it's always going to be "mit_kuerzel.csv", then there's no need for paste0, just use function() "mit_kuerzel.csv".
However, if you are intending to return a file named something based on the original input filename, one could do something like:
filename = function() {
paste0(tools::file_path_sans_ext(basename(input$upload$name)),
"_mit_kuerzel.",
tools::file_ext(input$upload$name))
},
to add _mit_kuerzel to the base portion of the uploaded filename. Note that the file in the content= section is never this name, the new_mit_kuerzel.csv is the filename offered to the downloading browser as a suggestion, that is all.
(Optional) You are using a .csv file extension in the downloadHandler, but the default for vroom::vroom_write is to use delim = "\t", which is not a CSV. I suggest either adding delim = ";" (or similar), or changing the returned filename extension to .tsv instead.

How define Server for Copy/Paste regions as input in R/Shiny?

I have a shiny which can be used to overlap between query regions and a given data table (e.g. DF). I put two options for uploading query data 1) as .bed format and 2) inserting data as copy/paste.
The shiny works well with uploading .bed file but I am not sure how can I define Server for copy/paste (text) data.
Thank you in advance for any suggestion!
DF<- data.table(chr=c("chr1","chr2"),start=c(10,20),end=c(20,30))%>% setkey(chr, start, end)
text<- data.table(chr=c("chr1","chr2"),start=c(15,25),end=c(15,30))%>% setkey(chr, start, end)
ui <- fluidPage(
sidebarLayout(
sidebarPanel (
p(strong ("Find overlap between query file and data"),style = "color:blue;"),
br(),
selectInput("choose","Choose file source",choices = c("file","text"),selected = "file"),
conditionalPanel("input.choose=='file'",
fileInput("query.file", "Upload genomic coordinates in .bed
format:",multiple = F,accept = ".bed")),
conditionalPanel("input.choose=='text'",
textAreaInput("query.text", "Enter genomic coordinates:")),
actionButton("run", "run"),
width = "2"),
mainPanel(
dataTableOutput("DFtable"),
dataTableOutput("overlap_table"))
)
)
server <- function (input, output, session) {
## Read user .bed file
user_query.file <- reactive({
req(input$query.file)
ext <- tools::file_ext(input$query.file$name)
switch(ext,
bed = fread(input$query.file$datapath,header=F)%>%
dplyr::rename (chr =V1, start=V2, end=V3) %>% setkey(chr, start, end)%>% unique()
)
})
## overlapping between query file and table
overlap <- eventReactive(input$run, {
req(input$run)
withProgress(message = 'Analysis in progress', value = 0, {
query.overlap<- foverlaps(user_query.file() ,DF, nomatch = 0) %>%
unique()
})
})
## output
output$DFtable<- renderDataTable({ DF })
output$overlap_table <- renderDT({overlap () })
}
shinyApp(ui, server)
Desire out put using TEXT input option:
chr start end i.start i.end
chr1 15 15 10 20
chr2 25 30 20 30
Not sure on how your copied text looks like, but assuming something like:
chr,start,end
chr1,10,20
chr4,34,56
All you need is to parse the text contents of the UI input and assigned it to DF variable. Your run event handler could look like:
## overlapping between query file and table
overlap <- eventReactive(input$run, {
req(input$run)
#Requiring text input and parsing it
req(input$query.text)
DF <- data.table(read.csv(text=input$query.text)) %>% setkey(chr, start, end)
withProgress(message = 'Analysis in progress', value = 0, {
query.overlap<- foverlaps(text ,DF, nomatch = 0) %>%
unique()
})
})
Then when clicking on the run button, the analysis is executed and the overlap reactive value is updated. If the comparison is always between file and text provided, you should also include a req(user_query.file()) to ensure the file has been provided and correctly parsed.

For Loop in RShiny: Warning: "Error in names: 0 arguments passed to ... which requires 1"

using RShiny/SQL for the first time so I'm sure I'm misunderstanding a fundament but none of the documentation is helping. I'm trying to:
(1) let the user choose which SQL table to load in
(2) submit a string of characters (protein names)
(3) return which protein names are in the chosen table
I've managed the first 2 fine but on the for loop I get '0 arguments passed to 'names' which requires one' and I'm not sure why. My code:
UI:
>library(shiny)
ui <- fluidPage(
titlePanel("TBD"),
sidebarLayout(
sidebarPanel(
selectInput("variable", "variable:",
list("Knoener" = "Knoener",
"Liz" = "Liz",
"Kula" = "Kula")),
actionButton("button1", "Click Me"),
textInput("names","Enter protein symbols"),
actionButton("button2", "Click Me"),
actionButton("button3", "Let's go!")
),
mainPanel(
textOutput("text1"),
textOutput("text2"),
textOutput("text3")
)
))
SERVER:
library("shiny")
library("DBI")
library("dplyr")
library("dbplyr")
library('pool')
loadData <- function(table) {
db <- dbConnect(MySQL(), dbname = "knoenerdb", host = "localhost",
user = "root",
password = "blahblah")
query <- sprintf("SELECT * FROM %s", table)
chosendata <- dbGetQuery(db, query)
dbDisconnect(db)
}
server <- function(input, output) {
chosendata <- observeEvent(input$button1, {
loadData(input$variable)
output$text1 <- renderText({paste("input is",input$variable)})})
names <- observeEvent( input$button2, {
names <- unlist(strsplit(input$names, ", "))
output$text2 <- renderText({paste("names are",names)})
})
observeEvent( input$button3, {
for(i in 1:length(names())){
if(names()[i] %in% chosendata()$proteins){
updated = c(updated,names()[i])
} else
updated = c(updated, "NULL")
}
output$text3 <- renderText({paste("matches are",updated)})
})
}
Thanks for the help!
My guess would be that you have some names clashing. Consider renaming text input names to something unique.
> names()
Error in names() : 0 arguments passed to 'names' which requires 1

For loop - doesn't work properly

I'm trying to use Indeed API to search for specific jobs and I faced a problem when for loop doesn't go through each iterations.
Here is the example of code that I used:
original_url_1 <- "http://api.indeed.com/ads/apisearch?publisher=750330686195873&format=json&q="
original_url_2 <-"&l=Canada&sort=date&radius=10&st=&jt=&start=0&limit=25&fromage=3&filter=&latlong=1&co=ca&chnl=&userip=69.46.99.196&useragent=Mozilla/%2F4.0%28Firefox%29&v=2"
keywords <- c("data+scientist", "data+analyst")
for(i in keywords) {
url <- paste0(original_url_1,i,original_url_2)
x <- as.data.frame(jsonlite::fromJSON(httr::content(httr::GET(url),
as = "text", encoding = "UTF-8")))
data <- rbind(data, x)
}
Url leads to JSON file and adding one of the keyword to the url will change the JSON file. So I'm trying to repeat this for all keywords and store the result in the dataframe. However, when I'm trying to use more keywords I'm getting the result only for a few first keywords.
original_url_1 <- "http://api.indeed.com/ads/apisearch?publisher=750330686195873&format=json&q="
original_url_2 <-"&l=Canada&sort=date&radius=10&st=&jt=&start=0&limit=25&fromage=3&filter=&latlong=1&co=ca&chnl=&userip=69.46.99.196&useragent=Mozilla/%2F4.0%28Firefox%29&v=2"
keywords <- c("data_scientist", "data+analyst")
data<-data.table(NULL)#initialization of object
for(i in keywords) {
url <- paste0(Original_url_1,i,Original_url_2)
x <- as.data.frame(jsonlite::fromJSON(httr::content(httr::GET(url),as = "text", encoding = "UTF-8")))
data <- rbind(data, x)
}
>dim(data)
[1] 39 31
Here is the correct code:
original_url_1 <- "http://api.indeed.com/ads/apisearch?publisher=750330686195873&format=json&q="
original_url_2 <-"&l=Canada&sort=date&radius=10&st=&jt=&start=0&limit=25&fromage=3&filter=&latlong=1&co=ca&chnl=&userip=69.46.99.196&useragent=Mozilla/%2F4.0%28Firefox%29&v=2"
keywords <- c("data+scientist", "data+analyst")
data <- data.frame()
for (i in keywords) {
tryCatch({url <- paste0(original_url_1,i,original_url_2)
x <- as.data.frame(jsonlite::fromJSON(httr::content(httr::GET(url),
as = "text", encoding = "UTF-8")))
data <- rbind(data, x)
}, error = function(t){})
}

Loading json encoded log files into R for analysis

I have a log file with each line a json-encoded entry:
{"requestId":"5550d","partnerId":false,"ip":"170.158.3.1", ... }
I tried reading each line, json_decode and then append to the dataframe:
loadLogs <- function(fileName) {
conn <- file(fileName, "r", blocking = FALSE)
linn <- readLines(conn)
long <- length(linn)
df = data.frame(requestId = character(0),
partnerId = character(0),
ip = character(0)
)
for (i in 1:long) {
jsonRow <- fromJSON(linn[i])
df <- rbind(df, data.frame(requestId = jsonRow$requestId,
partnerId = as.character(jsonRow$partnerId),
ip = jsonRow$ip
}
close(conn)
return(df)
}
The above code is extremely slow for large files though. Is there any way to speed this up? A few options I can think of at the moment:
pre-allocate the dataframe as its copying the entire data for a new append
using apply function on the json_decode
???
How would I do (1) and (2) in R? I'm new.
Thanks for looking at my question.