Package 'recogito' reference manual

Title:	Interactive Annotation of Text and Images
Description:	Annotate text with entities and the relations between them. Annotate areas of interest in images with your labels. Providing 'htmlwidgets' bindings to the 'recogito' <https://github.com/recogito/recogito-js> and 'annotorious' <https://github.com/recogito/annotorious> libraries.
Authors:	Jan Wijffels [aut, cre, cph], Vrije Universiteit Brussel - DIGI: Brussels Platform for Digital Humanities [cph], Pelagios Network [cph] (code in inst/htmlwidgets/lib), CodePlex Foundation [cph] (code in inst/htmlwidgets/lib/openseadragon-2.4.2), OpenSeadragon contributors [cph] (code in inst/htmlwidgets/lib/openseadragon-2.4.2)
Maintainer:	Jan Wijffels <[email protected]>
License:	BSD_3_clause + file LICENSE
Version:	0.2.1
Built:	2024-11-21 03:04:46 UTC
Source:	https://github.com/digi-vub/recogito

Annotate images with areas of interest

Description

Functionality to label areas in images

Usage

annotorious(
  inputId = "annotations",
  src,
  tags = c(),
  type = c("annotorious", "openseadragon", "openseadragon-notoolbar"),
  quickselector = TRUE,
  width = NULL,
  height = NULL,
  elementId = NULL,
  dependencies = NULL
)
annotorious(
  inputId = "annotations",
  src,
  tags = c(),
  type = c("annotorious", "openseadragon", "openseadragon-notoolbar"),
  quickselector = TRUE,
  width = NULL,
  height = NULL,
  elementId = NULL,
  dependencies = NULL
)

Arguments

`inputId`	character string with the name to use where annotations will be put into
`src`	character string with the image/url to annotate
`tags`	character vector of possible labels you want to use
`type`	either `'annotorious'`, `'openseadragon'`, `'openseadragon-notoolbar'` in order to allow zooming with openseadragon or not, with or without a toolbar
`quickselector`	logical indicating if for type `'openseadragon'` the possible tags should be shows as quick buttons to click. Defaults to `TRUE`.
`width`	passed on to `createWidget`
`height`	passed on to `createWidget`
`elementId`	passed on to `createWidget`
`dependencies`	passed on to `createWidget`

Value

An object of class htmlwidget as returned by createWidget

Shiny bindings for annotorious

Description

Output and render functions for using annotorious within Shiny applications.

Usage

annotoriousOutput(outputId, width = "100%", height = "400px")

renderAnnotorious(expr, env = parent.frame(), quoted = FALSE)

openseadragonOutput(outputId, width = "100%", height = "400px")

renderOpenSeaDragon(expr, env = parent.frame(), quoted = FALSE)

openseadragonOutputNoToolbar(outputId, width = "100%", height = "400px")

renderOpenSeaDragonNoToolbar(expr, env = parent.frame(), quoted = FALSE)
annotoriousOutput(outputId, width = "100%", height = "400px")

renderAnnotorious(expr, env = parent.frame(), quoted = FALSE)

openseadragonOutput(outputId, width = "100%", height = "400px")

renderOpenSeaDragon(expr, env = parent.frame(), quoted = FALSE)

openseadragonOutputNoToolbar(outputId, width = "100%", height = "400px")

renderOpenSeaDragonNoToolbar(expr, env = parent.frame(), quoted = FALSE)

Arguments

`outputId`	output variable to read from
`width`, `height`	Must be a valid CSS unit (like `'100%'`, `'400px'`, `'auto'`) or a number, which will be coerced to a string and have `'px'` appended.
`expr`	An expression that generates a annotorious
`env`	The environment in which to evaluate `expr`.
`quoted`	Is `expr` a quoted expression (with `quote()`)? This is useful if you want to save an expression in a variable.

Value

An output element for use in a Shiny user interface.
Consisting of a toggle button to switch between rectangle / polygon mode and the html-widget (id: outputId) which contains an image (id: outputId-img)

Examples

if(interactive() && require(shiny)){
##
## Annotorious using OpenSeaDragon, allowing to zoom in,
## to select an area, press shift and next select the area
##
library(shiny)
library(recogito)
urls <- paste("https://upload.wikimedia.org/",
              c("wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
                "wikipedia/commons/6/64/Cat_and_dog_standoff_%283926784260%29.jpg"),
              sep = "")
ui <- fluidPage(actionButton(inputId = "ui_switch", label = "Sample image"),
                openseadragonOutput(outputId = "anno"),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  current_image <- reactive({
    input$ui_switch
    list(url = sample(urls, size = 1))
  })
  output$anno <- renderOpenSeaDragon({
    info <- current_image()
    annotorious("annotations", tags = c("IMAGE", "TEXT"), src = info$url, type = "openseadragon")
  })
  output$annotation_result <- renderPrint({
    read_annotorious(input$annotations)
  })
}
shinyApp(ui, server)

##
## Annotorious using OpenSeaDragon, allowing to zoom in, no selection possibilities
## showing how to load a local image
##
library(shiny)
library(recogito)
url <- system.file(package = "recogito", "examples", "Pamphlet_dutch_tulipomania_1637.jpg")
addResourcePath(prefix = "img", directoryPath = dirname(url))
ui <- fluidPage(openseadragonOutputNoToolbar(outputId = "anno", width = "100%", height = "250px"))
server <- function(input, output) {
  output$anno <- renderOpenSeaDragonNoToolbar({
    annotorious("annotations", src = sprintf("img/%s", basename(url)),
                 type = "openseadragon-notoolbar")
  })
}
shinyApp(ui, server)

##
## Annotorious without openseadragon
##
library(shiny)
library(recogito)
url <- paste("https://upload.wikimedia.org/",
             "wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
             sep = "")

ui <- fluidPage(annotoriousOutput(outputId = "anno", height = "600px"),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  output$anno <- renderAnnotorious({
    annotorious("annotations", tags = c("IMAGE", "TEXT"), src = url, type = "annotorious")
  })
  output$annotation_result <- renderPrint({
    read_annotorious(input$annotations)
  })
}
shinyApp(ui, server)

##
## Annotorious, without openseadragon changing the url
##
library(shiny)
library(recogito)
urls <- paste("https://upload.wikimedia.org/",
              c("wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
                "wikipedia/commons/6/64/Cat_and_dog_standoff_%283926784260%29.jpg"),
              sep = "")

ui <- fluidPage(actionButton(inputId = "ui_switch", label = "Sample image"),
                annotoriousOutput(outputId = "anno", height = "600px"),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  current_image <- reactive({
    input$ui_switch
    list(url = sample(urls, size = 1))
  })
  output$anno <- renderAnnotorious({
    info <- current_image()
    annotorious("annotations", tags = c("IMAGE", "TEXT"), src = info$url, type = "annotorious")
  })
  output$annotation_result <- renderPrint({
    read_annotorious(input$annotations)
  })
}
shinyApp(ui, server)

}
if(interactive() && require(shiny)){
##
## Annotorious using OpenSeaDragon, allowing to zoom in,
## to select an area, press shift and next select the area
##
library(shiny)
library(recogito)
urls <- paste("https://upload.wikimedia.org/",
              c("wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
                "wikipedia/commons/6/64/Cat_and_dog_standoff_%283926784260%29.jpg"),
              sep = "")
ui <- fluidPage(actionButton(inputId = "ui_switch", label = "Sample image"),
                openseadragonOutput(outputId = "anno"),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  current_image <- reactive({
    input$ui_switch
    list(url = sample(urls, size = 1))
  })
  output$anno <- renderOpenSeaDragon({
    info <- current_image()
    annotorious("annotations", tags = c("IMAGE", "TEXT"), src = info$url, type = "openseadragon")
  })
  output$annotation_result <- renderPrint({
    read_annotorious(input$annotations)
  })
}
shinyApp(ui, server)

##
## Annotorious using OpenSeaDragon, allowing to zoom in, no selection possibilities
## showing how to load a local image
##
library(shiny)
library(recogito)
url <- system.file(package = "recogito", "examples", "Pamphlet_dutch_tulipomania_1637.jpg")
addResourcePath(prefix = "img", directoryPath = dirname(url))
ui <- fluidPage(openseadragonOutputNoToolbar(outputId = "anno", width = "100%", height = "250px"))
server <- function(input, output) {
  output$anno <- renderOpenSeaDragonNoToolbar({
    annotorious("annotations", src = sprintf("img/%s", basename(url)),
                 type = "openseadragon-notoolbar")
  })
}
shinyApp(ui, server)

##
## Annotorious without openseadragon
##
library(shiny)
library(recogito)
url <- paste("https://upload.wikimedia.org/",
             "wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
             sep = "")

ui <- fluidPage(annotoriousOutput(outputId = "anno", height = "600px"),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  output$anno <- renderAnnotorious({
    annotorious("annotations", tags = c("IMAGE", "TEXT"), src = url, type = "annotorious")
  })
  output$annotation_result <- renderPrint({
    read_annotorious(input$annotations)
  })
}
shinyApp(ui, server)

##
## Annotorious, without openseadragon changing the url
##
library(shiny)
library(recogito)
urls <- paste("https://upload.wikimedia.org/",
              c("wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
                "wikipedia/commons/6/64/Cat_and_dog_standoff_%283926784260%29.jpg"),
              sep = "")

ui <- fluidPage(actionButton(inputId = "ui_switch", label = "Sample image"),
                annotoriousOutput(outputId = "anno", height = "600px"),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  current_image <- reactive({
    input$ui_switch
    list(url = sample(urls, size = 1))
  })
  output$anno <- renderAnnotorious({
    info <- current_image()
    annotorious("annotations", tags = c("IMAGE", "TEXT"), src = info$url, type = "annotorious")
  })
  output$annotation_result <- renderPrint({
    read_annotorious(input$annotations)
  })
}
shinyApp(ui, server)

}

Crop annotations to a bounding box

Description

Crop annotations to a bounding box

Usage

ocv_crop_annotorious(data, bbox)
ocv_crop_annotorious(data, bbox)

Arguments

`data`	an object as returned by `read_annotorious`
`bbox`	a vector with elements x, y, xmax, ymax

Value

data where column polygon and the rectangle information in x, y, width, height is limited to the provided bounding box

Examples


library(opencv)
data(openseadragon_areas)

url  <- attr(openseadragon_areas, "src")
img  <- ocv_read(url)
bbox <- ocv_info(img)
bbox <- c(xmin = 0, ymin = 0, xmax = bbox$width - 1, ymax = bbox$height - 1)
x    <- ocv_crop_annotorious(data = openseadragon_areas)
x    <- ocv_crop_annotorious(data = openseadragon_areas, bbox = bbox)

img
area <- x[2, ]
ocv_polygon(img, pts = area$polygon[[1]], crop = TRUE)
area <- x[1, ]
ocv_rectangle(img, x = area$x, y = area$y, width = area$width, height = area$height)
area <- x[3, ]
ocv_rectangle(img, x = area$x, y = area$y, width = area$width, height = area$height)

library(opencv)
data(openseadragon_areas)

url  <- attr(openseadragon_areas, "src")
img  <- ocv_read(url)
bbox <- ocv_info(img)
bbox <- c(xmin = 0, ymin = 0, xmax = bbox$width - 1, ymax = bbox$height - 1)
x    <- ocv_crop_annotorious(data = openseadragon_areas)
x    <- ocv_crop_annotorious(data = openseadragon_areas, bbox = bbox)

img
area <- x[2, ]
ocv_polygon(img, pts = area$polygon[[1]], crop = TRUE)
area <- x[1, ]
ocv_rectangle(img, x = area$x, y = area$y, width = area$width, height = area$height)
area <- x[3, ]
ocv_rectangle(img, x = area$x, y = area$y, width = area$width, height = area$height)

Extract the areas of interests of an image

Description

Extract the areas of interests of an image

Usage

ocv_read_annotorious(data, image)
ocv_read_annotorious(data, image)

Arguments

`data`	an object as returned by `read_annotorious`
`image`	an ocv image object

Value

a list of ocv images with the extracted areas of interest

Examples


library(opencv)
library(magick)
data(openseadragon_areas)

url  <- attr(openseadragon_areas, "src")
img  <- ocv_read(url)

areas <- ocv_read_annotorious(data = openseadragon_areas, image = img)
areas[[1]]
areas[[2]]
img <- lapply(areas, FUN = function(x) image_read(ocv_bitmap(x)))
img <- do.call(c, img)
img <- image_append(img, stack = FALSE)
image_resize(img, "x200")

library(opencv)
library(magick)
data(openseadragon_areas)

url  <- attr(openseadragon_areas, "src")
img  <- ocv_read(url)

areas <- ocv_read_annotorious(data = openseadragon_areas, image = img)
areas[[1]]
areas[[2]]
img <- lapply(areas, FUN = function(x) image_read(ocv_bitmap(x)))
img <- do.call(c, img)
img <- image_append(img, stack = FALSE)
image_resize(img, "x200")

A dataset of annotations using openseadragon

Description

A dataset of annotations using openseadragon

Examples

data(openseadragon_areas)
openseadragon_areas
attr(openseadragon_areas, "src")
data(openseadragon_areas)
openseadragon_areas
attr(openseadragon_areas, "src")

Parse annotorious annotations

Description

Parse annotorious annotations

Usage

read_annotorious(x, src = character())
read_annotorious(x, src = character())

Arguments

`x`	a character string with json as returned by the htmlwidget
`src`	a character string with the image src which was used in `x`

Value

a data.frame with annotations with columns: id, type, label, comment, x, y, width, height, polygon and an attribute src with the provided src

Examples

url <- paste("https://upload.wikimedia.org/",
             "wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
             sep = "")
url <- system.file(package = "recogito", "examples", "Pamphlet_dutch_tulipomania_1637.jpg")
x <- '[
{
"type":"Annotation",
"body":[{"type":"TextualBody","value":"IMAGE","purpose":"tagging"}],
"target":{"selector":{
  "type":"FragmentSelector",
  "conformsTo":"http://www.w3.org/TR/media-frags/",
  "value":"xywh=pixel:41,249.5234375,371,245"}},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#58f0096c-4675-4ea8-9f38-bffce0887ab8"
},
{
"type":"Annotation",
"body":[{"type":"TextualBody","value":"TEXT","purpose":"tagging"}],
"target":{"selector":{
  "type":"FragmentSelector",
  "conformsTo":"http://www.w3.org/TR/media-frags/",
  "value":"xywh=pixel:46,5.523437976837158,371,239.99999952316284"}},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#50035dda-c62b-4f30-bf95-1879d60288a5"}]'
anno <- read_annotorious(x, src = url)
anno


library(magick)
img  <- image_read(url)
area <- head(anno, n = 1)
image_crop(img, geometry_area(x = area$x, y = area$y,
                              width = area$width, height = area$height))
area <- subset(anno, type == "RECTANGLE")
allrectangles <- Map(
  x      = area$x,
  y      = area$y,
  width  = area$width,
  height = area$height,
  f = function(x, y, width, height){
    image_crop(img, geometry_area(x = x, y = y, width = width, height = height))
})
allrectangles <- do.call(c, allrectangles)
allrectangles



x <- '[
{
  "type":"Annotation",
  "body":[{"type":"TextualBody","value":"IMAGE","purpose":"tagging"}],
  "target":{"selector":{
    "type":"FragmentSelector",
    "conformsTo":"http://www.w3.org/TR/media-frags/",
    "value":"xywh=pixel:43,244.5234375,362,252"
    }},
 "@context":"http://www.w3.org/ns/anno.jsonld",
 "id":"#4eaa8788-0c7e-42d2-b004-4d66b57018a1"},
{
  "type":"Annotation",
  "body":[{"type":"TextualBody","value":"TEXT","purpose":"tagging"}],
  "target":{"selector":{
    "type":"SvgSelector",
    "value":"<svg>
    <polygon points=\\\"75,4 75,58 32,95 32,194 410,195 391,70 373,63 368,3 222,1.5\\\">
    </polygon></svg>"}},
  "@context":"http://www.w3.org/ns/anno.jsonld",
  "id":"#8bf0a557-c847-4a07-91bc-68a98c499615"}]'
x    <- gsub(x, pattern = "\n", replacement = "")
anno <- read_annotorious(x, src = url)
anno
anno$polygon


library(opencv)
img  <- ocv_read(url)
area <- subset(anno, type == "POLYGON")
ocv_polygon(img, pts = area$polygon[[1]])

url <- paste("https://upload.wikimedia.org/",
             "wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
             sep = "")
url <- system.file(package = "recogito", "examples", "Pamphlet_dutch_tulipomania_1637.jpg")
x <- '[
{
"type":"Annotation",
"body":[{"type":"TextualBody","value":"IMAGE","purpose":"tagging"}],
"target":{"selector":{
  "type":"FragmentSelector",
  "conformsTo":"http://www.w3.org/TR/media-frags/",
  "value":"xywh=pixel:41,249.5234375,371,245"}},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#58f0096c-4675-4ea8-9f38-bffce0887ab8"
},
{
"type":"Annotation",
"body":[{"type":"TextualBody","value":"TEXT","purpose":"tagging"}],
"target":{"selector":{
  "type":"FragmentSelector",
  "conformsTo":"http://www.w3.org/TR/media-frags/",
  "value":"xywh=pixel:46,5.523437976837158,371,239.99999952316284"}},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#50035dda-c62b-4f30-bf95-1879d60288a5"}]'
anno <- read_annotorious(x, src = url)
anno


library(magick)
img  <- image_read(url)
area <- head(anno, n = 1)
image_crop(img, geometry_area(x = area$x, y = area$y,
                              width = area$width, height = area$height))
area <- subset(anno, type == "RECTANGLE")
allrectangles <- Map(
  x      = area$x,
  y      = area$y,
  width  = area$width,
  height = area$height,
  f = function(x, y, width, height){
    image_crop(img, geometry_area(x = x, y = y, width = width, height = height))
})
allrectangles <- do.call(c, allrectangles)
allrectangles



x <- '[
{
  "type":"Annotation",
  "body":[{"type":"TextualBody","value":"IMAGE","purpose":"tagging"}],
  "target":{"selector":{
    "type":"FragmentSelector",
    "conformsTo":"http://www.w3.org/TR/media-frags/",
    "value":"xywh=pixel:43,244.5234375,362,252"
    }},
 "@context":"http://www.w3.org/ns/anno.jsonld",
 "id":"#4eaa8788-0c7e-42d2-b004-4d66b57018a1"},
{
  "type":"Annotation",
  "body":[{"type":"TextualBody","value":"TEXT","purpose":"tagging"}],
  "target":{"selector":{
    "type":"SvgSelector",
    "value":"<svg>
    <polygon points=\\\"75,4 75,58 32,95 32,194 410,195 391,70 373,63 368,3 222,1.5\\\">
    </polygon></svg>"}},
  "@context":"http://www.w3.org/ns/anno.jsonld",
  "id":"#8bf0a557-c847-4a07-91bc-68a98c499615"}]'
x    <- gsub(x, pattern = "\n", replacement = "")
anno <- read_annotorious(x, src = url)
anno
anno$polygon


library(opencv)
img  <- ocv_read(url)
area <- subset(anno, type == "POLYGON")
ocv_polygon(img, pts = area$polygon[[1]])

Parse recogito annotations

Description

Parse recogito annotations

Usage

read_recogito(x, text = character())
read_recogito(x, text = character())

Arguments

`x`	a character string with json as returned by the htmlwidget
`text`	a character string with the text which was used in `x`

Value

a data.frame with annotations with columns: id, type, label, chunk_text, chunk_start, chunk_end, relation_from, relation_to, chunk_comment and an attribute text with the provided text

Examples

x <- '[
{
"type":"Annotation",
"body":[
   {"type":"TextualBody","value":"sdfsd","purpose":"commenting"},
   {"type":"TextualBody","value":"Person","purpose":"tagging"}],
"target":{"selector":[
  {"type":"TextQuoteSelector","exact":"ngenious hero"},
  {"type":"TextPositionSelector","start":42,"end":55}]},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#a4ea53d4-69f3-4392-a3dd-cbb7e9ad50cb"
},
{
"type":"Annotation",
"body":[{"type":"TextualBody","value":"Person","purpose":"tagging"},
  {"type":"TextualBody","value":"Location","purpose":"tagging"}],
"target":{"selector":[{"type":"TextQuoteSelector","exact":"far and"},
  {"type":"TextPositionSelector","start":70,"end":77}]},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#d7050196-2537-42bf-9d1b-a3f9e4c9fbc6"
}
]'
read_recogito(x)
x <- '[
{
"type":"Annotation",
"body":[
   {"type":"TextualBody","value":"sdfsd","purpose":"commenting"},
   {"type":"TextualBody","value":"Person","purpose":"tagging"}],
"target":{"selector":[
  {"type":"TextQuoteSelector","exact":"ngenious hero"},
  {"type":"TextPositionSelector","start":42,"end":55}]},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#a4ea53d4-69f3-4392-a3dd-cbb7e9ad50cb"
},
{
"type":"Annotation",
"body":[{"type":"TextualBody","value":"Person","purpose":"tagging"},
  {"type":"TextualBody","value":"Location","purpose":"tagging"}],
"target":{"selector":[{"type":"TextQuoteSelector","exact":"far and"},
  {"type":"TextPositionSelector","start":70,"end":77}]},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#d7050196-2537-42bf-9d1b-a3f9e4c9fbc6"
}
]'
read_recogito(x)

Annotate text with tags and relations

Description

Functionality to tag text with entities and relations between these

Usage

recogito(
  inputId = "annotations",
  text,
  type = c("relations", "tags"),
  tags = c("Location", "Person", "Place", "Other"),
  mode = c("html", "pre"),
  annotations = "{}",
  width = NULL,
  height = NULL,
  elementId = NULL,
  dependencies = NULL
)
recogito(
  inputId = "annotations",
  text,
  type = c("relations", "tags"),
  tags = c("Location", "Person", "Place", "Other"),
  mode = c("html", "pre"),
  annotations = "{}",
  width = NULL,
  height = NULL,
  elementId = NULL,
  dependencies = NULL
)

Arguments

`inputId`	character string with the name to use where annotations will be put into
`text`	character string with the text to annotate
`type`	either 'relations' or 'tags' in order to label relations between tags or only plain tags
`tags`	character vector of possible tags
`mode`	either 'html' or 'pre'
`annotations`	character string with a predefined set of annotations
`width`	passed on to `createWidget`
`height`	passed on to `createWidget`
`elementId`	passed on to `createWidget`
`dependencies`	passed on to `createWidget`

Value

An object of class htmlwidget as returned by createWidget

Examples

txt <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
x   <- recogito(inputId = "annotations", txt)
x
x   <- recogito(inputId = "annotations", txt, type = "tags",
                tags = c("LOCATION", "TIME", "PERSON"))
x
txt <- "Lorem ipsum dolor sit amet consectetur adipiscing elit Quisque tellus urna
  placerat in tortor ac imperdiet sollicitudin mi Integer vel dolor mollis feugiat
  sem eu porttitor elit Sed aliquam urna sed placerat euismod In risus sem ornare
  nec malesuada eu ornare quis dui Nunc finibus fermentum sollicitudin Fusce vel
  imperdiet mi ac faucibus leo Cras massa massa ultricies et justo vitae molestie
  auctor turpis Vestibulum euismod porta risus euismod dapibus Nullam facilisis
  ipsum sed est tempor et aliquam sapien auctor Aliquam velit ligula convallis a
  dui id varius bibendum quam Cras malesuada nec justo sed
  aliquet Fusce urna magna malesuada"
x   <- recogito(inputId = "annotations", txt)
x
x   <- recogito(inputId = "annotations", txt, type = "tags",
                tags = c("LOCATION", "TIME", "PERSON", "OTHER"))
x

##
## Color the tags by specifying CSS - they should have .tag-{TAGLABEL}
##
library(htmltools)
cat(readLines(system.file(package = "recogito", "examples", "example.css")), sep = "\n")
tagsetcss <- htmlDependency(name = "mytagset", version = "1.0",
                            src = system.file(package = "recogito", "examples"),
                            stylesheet = "example.css")
x   <- recogito(inputId = "annotations", txt,
                tags = c("LOCATION", "TIME", "PERSON", "OTHER"),
                dependencies = tagsetcss)
x
txt <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
x   <- recogito(inputId = "annotations", txt)
x
x   <- recogito(inputId = "annotations", txt, type = "tags",
                tags = c("LOCATION", "TIME", "PERSON"))
x
txt <- "Lorem ipsum dolor sit amet consectetur adipiscing elit Quisque tellus urna
  placerat in tortor ac imperdiet sollicitudin mi Integer vel dolor mollis feugiat
  sem eu porttitor elit Sed aliquam urna sed placerat euismod In risus sem ornare
  nec malesuada eu ornare quis dui Nunc finibus fermentum sollicitudin Fusce vel
  imperdiet mi ac faucibus leo Cras massa massa ultricies et justo vitae molestie
  auctor turpis Vestibulum euismod porta risus euismod dapibus Nullam facilisis
  ipsum sed est tempor et aliquam sapien auctor Aliquam velit ligula convallis a
  dui id varius bibendum quam Cras malesuada nec justo sed
  aliquet Fusce urna magna malesuada"
x   <- recogito(inputId = "annotations", txt)
x
x   <- recogito(inputId = "annotations", txt, type = "tags",
                tags = c("LOCATION", "TIME", "PERSON", "OTHER"))
x

##
## Color the tags by specifying CSS - they should have .tag-{TAGLABEL}
##
library(htmltools)
cat(readLines(system.file(package = "recogito", "examples", "example.css")), sep = "\n")
tagsetcss <- htmlDependency(name = "mytagset", version = "1.0",
                            src = system.file(package = "recogito", "examples"),
                            stylesheet = "example.css")
x   <- recogito(inputId = "annotations", txt,
                tags = c("LOCATION", "TIME", "PERSON", "OTHER"),
                dependencies = tagsetcss)
x

Shiny bindings for recogito

Description

Output and render functions for using recogito within Shiny applications and interactive Rmd documents.

Usage

recogitoOutput(outputId, width = "100%", height = "400px")

renderRecogito(expr, env = parent.frame(), quoted = FALSE)

recogitotagsonlyOutput(outputId, width = "100%", height = "400px")

renderRecogitotagsonly(expr, env = parent.frame(), quoted = FALSE)
recogitoOutput(outputId, width = "100%", height = "400px")

renderRecogito(expr, env = parent.frame(), quoted = FALSE)

recogitotagsonlyOutput(outputId, width = "100%", height = "400px")

renderRecogitotagsonly(expr, env = parent.frame(), quoted = FALSE)

Arguments

`outputId`	output variable to read from
`width`, `height`	Must be a valid CSS unit (like `'100%'`, `'400px'`, `'auto'`) or a number, which will be coerced to a string and have `'px'` appended.
`expr`	An expression that generates a recogito
`env`	The environment in which to evaluate `expr`.
`quoted`	Is `expr` a quoted expression (with `quote()`)? This is useful if you want to save an expression in a variable.

Value

An output element for use in a Shiny user interface.
Consisting of a div of class plaintext which contains an optional toggle button to switch between annotation / relation mode (id: outputId-toggle) and the html-widget (id: outputId)

Examples

if(interactive() && require(shiny)){

##
## Tagging only, no relations
##
library(shiny)
library(recogito)
txt <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
ui <- fluidPage(tags$h3("Provide some text to annotate"),
                textAreaInput(inputId = "ui_text", label = "Provide some text", value = txt),
                tags$h3("Annotation area"),
                recogitotagsonlyOutput(outputId = "annotation_text"),
                tags$hr(),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  output$annotation_text <- renderRecogitotagsonly({
    recogito("annotations", text = input$ui_text, tags = c("LOCATION", "TIME", "PERSON"))
  })
  output$annotation_result <- renderPrint({
    read_recogito(input$annotations)
  })
}
shinyApp(ui, server)

##
## Tagging and relations
##
library(shiny)
library(recogito)
txt <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
ui <- fluidPage(tags$h3("Provide some text to annotate"),
                textAreaInput(inputId = "ui_text", label = "Provide some text", value = txt),
                tags$h3("Annotation area"),
                recogitoOutput(outputId = "annotation_text"),
                tags$hr(),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  output$annotation_text <- renderRecogito({
    recogito("annotations", text = input$ui_text, tags = c("LOCATION", "TIME", "PERSON"))
  })
  output$annotation_result <- renderPrint({
    read_recogito(input$annotations)
  })
}
shinyApp(ui, server)

}

recogitoOutput(outputId = "annotation_text")
recogitotagsonlyOutput(outputId = "annotation_text")
if(interactive() && require(shiny)){

##
## Tagging only, no relations
##
library(shiny)
library(recogito)
txt <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
ui <- fluidPage(tags$h3("Provide some text to annotate"),
                textAreaInput(inputId = "ui_text", label = "Provide some text", value = txt),
                tags$h3("Annotation area"),
                recogitotagsonlyOutput(outputId = "annotation_text"),
                tags$hr(),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  output$annotation_text <- renderRecogitotagsonly({
    recogito("annotations", text = input$ui_text, tags = c("LOCATION", "TIME", "PERSON"))
  })
  output$annotation_result <- renderPrint({
    read_recogito(input$annotations)
  })
}
shinyApp(ui, server)

##
## Tagging and relations
##
library(shiny)
library(recogito)
txt <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
ui <- fluidPage(tags$h3("Provide some text to annotate"),
                textAreaInput(inputId = "ui_text", label = "Provide some text", value = txt),
                tags$h3("Annotation area"),
                recogitoOutput(outputId = "annotation_text"),
                tags$hr(),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  output$annotation_text <- renderRecogito({
    recogito("annotations", text = input$ui_text, tags = c("LOCATION", "TIME", "PERSON"))
  })
  output$annotation_result <- renderPrint({
    read_recogito(input$annotations)
  })
}
shinyApp(ui, server)

}

recogitoOutput(outputId = "annotation_text")
recogitotagsonlyOutput(outputId = "annotation_text")

Package 'recogito'

Help Index

Annotate images with areas of interest

Description

Usage

Arguments

Value

See Also

Shiny bindings for annotorious

Description

Usage

Arguments

Value

Examples

Crop annotations to a bounding box

Description

Usage

Arguments

Value

Examples

Extract the areas of interests of an image

Description

Usage

Arguments

Value

Examples

A dataset of annotations using openseadragon

Description

Examples

Parse annotorious annotations

Description

Usage

Arguments

Value

Examples

Parse recogito annotations

Description

Usage

Arguments

Value

Examples

Annotate text with tags and relations

Description

Usage

Arguments

Value

See Also

Examples

Shiny bindings for recogito

Description

Usage

Arguments

Value

Examples