Package 'bscui' reference manual

Title:	Build SVG Custom User Interface
Description:	Render SVG as interactive figures to display contextual information, with selectable and clickable user interface elements. These figures can be seamlessly integrated into 'rmarkdown' and 'Quarto' documents, as well as 'shiny' applications, allowing manipulation of elements and reporting actions performed on them. Additional features include pan, zoom in/out functionality, and the ability to export the figures in SVG or PNG formats.
Authors:	Patrice Godard [aut, cre, cph]
Maintainer:	Patrice Godard <[email protected]>
License:	GPL-3
Version:	0.1.5
Built:	2024-11-03 04:05:50 UTC
Source:	https://github.com/patzaw/bscui

Add an SVG element to the UI

Description

Add an SVG element to the UI

Usage

add_bscui_element(proxy, id, svg_txt, ui_type = NULL, title = NULL)
add_bscui_element(proxy, id, svg_txt, ui_type = NULL, title = NULL)

Arguments

`proxy`	a `bscui_Proxy` object
`id`	the identifier of the element to add (will replace the id attribute of the provided svg if any)
`svg_txt`	a character with SVG code of one element and its children
`ui_type`	either "selectable", "button" or "none". If NULL (default), the element won't be available as UI
`title`	a description of the element to display on mouseover event

Value

the provided proxy object

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Build SVG Custom User Interface

Description

Build SVG Custom User Interface

Usage

bscui(
  svg_txt,
  sanitize_attributes = TRUE,
  width = NULL,
  height = NULL,
  elementId = NULL
)
bscui(
  svg_txt,
  sanitize_attributes = TRUE,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

`svg_txt`	a character with SVG code
`sanitize_attributes`	logical indicating if '<' and '>' characters in element attributes must be replaced by text
`width`, `height`	widget width: must be a valid CSS unit (like `'100\%'`, `'400px'`, `'auto'`) or a number, which will be coerced to a string and have `'px'` appended.
`elementId`	hmtl identifier of the widget

Value

An htmlwidget object

Examples

##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}
##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}

'shiny' bindings for bscui

Description

Output and render functions for using bscui within 'shiny' applications.

Usage

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

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

renderBscui(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 bscui
`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.

Details

The bscuiProxy() function can be used to allow user interface dynamic updates.

Value

An output or render function that enables the use of the widget within 'shiny' applications.

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Manipulate an existing bscui instance in a 'shiny' app

Description

Manipulate an existing bscui instance in a 'shiny' app

Usage

bscuiProxy(shinyId, session = shiny::getDefaultReactiveDomain())
bscuiProxy(shinyId, session = shiny::getDefaultReactiveDomain())

Arguments

`shinyId`	single-element character vector indicating the 'shiny' output ID of the UI to modify
`session`	the 'shiny' session object to which the UI belongs; usually the default value will suffice

Details

This function creates a proxy object that can be used to manipulate an existing bscui instance in a 'shiny' app using different methods:

update_bscui_ui_elements: change type and title of elements
update_bscui_styles: set style of UI elements
update_bscui_attributes set attributes of a UI element
update_bscui_selection: chose selected elements
click_bscui_element: trigger a single or double click on a UI element
order_bscui_elements: change elements order (e.g. move them forward)
add_bscui_element: add an SVG element to the UI
remove_bscui_elements: remove SVG elements from the UI
get_bscui_svg: get the displayed SVG in R session

Value

A bscui_Proxy object with an "id" and a "session" slot.

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Trigger a click event on a clickable element

Description

Trigger a click event on a clickable element

Usage

click_bscui_element(proxy, element_id, dbl_click = FALSE)
click_bscui_element(proxy, element_id, dbl_click = FALSE)

Arguments

`proxy`	a `bscui_Proxy` object
`element_id`	element identifier on which the click will be triggered
`dbl_click`	logical indicating the type of click (default: FALSE => single click is triggered)

Value

the provided proxy object

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Save a bscui widget to an image file

Description

Save a bscui widget to an image file

Usage

export_bscui_to_image(
  widget,
  file,
  selector = ".bscui",
  zoom = 1,
  quiet = TRUE,
  ...
)
export_bscui_to_image(
  widget,
  file,
  selector = ".bscui",
  zoom = 1,
  quiet = TRUE,
  ...
)

Arguments

`widget`	a `bscui` object
`file`	name of output file. Should end with an image file type (.png, .jpg, .jpeg, or .webp) or .pdf.
`selector`	(`webshot2::webshot()`) one or more CSS selectors specifying a DOM element to set the clipping rectangle to (default: ".bscui").
`zoom`	(`webshot2::webshot()`) If TRUE (default), status updates via console messages are suppressed.
`quiet`	(`webshot2::webshot()`) a number specifying the zoom factor.
`...`	additional parameters for `webshot2::webshot()` suppressed.

Value

Invisibly returns the normalized path to the image. The character vector will have a class of "webshot".

Examples

##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}
##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}

Get the displayed SVG

Description

Get the displayed SVG

Usage

get_bscui_svg(proxy)
get_bscui_svg(proxy)

Arguments

proxy

a bscui_Proxy object

Value

the provided proxy object

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Change element order in the SVG

Description

Change element order in the SVG

Usage

order_bscui_elements(
  proxy,
  element_ids,
  where = c("front", "back", "forward", "backward")
)
order_bscui_elements(
  proxy,
  element_ids,
  where = c("front", "back", "forward", "backward")
)

Arguments

`proxy`	a `bscui_Proxy` object
`element_ids`	the identifiers of the element to move
`where`	where to move the elements (default: "front")

Value

the provided proxy object

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Remove SVG elements from the UI

Description

Remove SVG elements from the UI

Usage

remove_bscui_elements(proxy, element_ids)
remove_bscui_elements(proxy, element_ids)

Arguments

`proxy`	a `bscui_Proxy` object
`element_ids`	the identifiers of the elements to remove

Value

the provided proxy object

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Set attributes of elements of a bscui widget

Description

Set attributes of elements of a bscui widget

Usage

set_bscui_attributes(
  widget,
  element_attributes,
  to_ignore = NULL,
  targeted_tags = widget$x$structure_shapes,
  append = FALSE
)
set_bscui_attributes(
  widget,
  element_attributes,
  to_ignore = NULL,
  targeted_tags = widget$x$structure_shapes,
  append = FALSE
)

Arguments

`widget`	a `bscui` object
`element_attributes`	a data frame with an id column providing the element identifier and one column per attribute name.
`to_ignore`	identifiers of elements to ignore: if those elements are children of elements to update they won't be updated
`targeted_tags`	targeted_tags affected tag names (by default: structure_shapes of the scui object)
`append`	if TRUE the value will be concatenate with the existing value

Value

The modified bscui object

Examples

##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}
##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}

Set options of bscui widget

Description

Set options of bscui widget

Usage

set_bscui_options(
  widget,
  show_menu,
  menu_width,
  zoom_min,
  zoom_max,
  zoom_step,
  clip,
  default_png_scale,
  selection_color,
  selection_opacity,
  selection_width,
  hover_color,
  hover_opacity,
  hover_width,
  structure_shapes,
  dblclick_timeout,
  hover_timeout,
  width,
  height
)
set_bscui_options(
  widget,
  show_menu,
  menu_width,
  zoom_min,
  zoom_max,
  zoom_step,
  clip,
  default_png_scale,
  selection_color,
  selection_opacity,
  selection_width,
  hover_color,
  hover_opacity,
  hover_width,
  structure_shapes,
  dblclick_timeout,
  hover_timeout,
  width,
  height
)

Arguments

`widget`	a `bscui` object
`show_menu`	if TRUE (default) control menu will be available
`menu_width`	css width value (default: "30px")
`zoom_min`	smallest zoom value (default: 0.5)
`zoom_max`	largest zoom value (default: 20)
`zoom_step`	zooming step: the larger the faster (default: 1.1)
`clip`	if TRUE (default: FALSE), when the current zoom is 1, the viewBox is automatically set to its original state (the drawing cannot be moved)
`default_png_scale`	default value for scaling PNG export (default: 1)
`selection_color`	color used to highlight selection (default: "orange")
`selection_opacity`	opacity of selection highlight (default: 0.5)
`selection_width`	the additional stroke width to apply on selection (default: 4)
`hover_color`	a list of colors used to highlight hovered elements (default: `list(button="yellow", selectable="cyan", none="transparent")`)
`hover_opacity`	opacity of hovered highlight (default: 0.5)
`hover_width`	the additional stroke width to apply on hover (default: 4)
`structure_shapes`	SVG shapes to considered as concrete drawing (default: `c("rect", "circle", "ellipse", "line", "polyline", "polygon", "path")`: "text" excluded)
`dblclick_timeout`	minimum time in ms between 2 independant clicks (default: 250)
`hover_timeout`	time in ms before update hovered element (default: 100)
`width`, `height`	widget width: must be a valid CSS unit (like `'100\%'`, `'400px'`, `'auto'`) or a number, which will be coerced to a string and have `'px'` appended.

Value

The modified bscui object

Examples

##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}
##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}

Pre-select UI elements in a bscui widget

Description

Pre-select UI elements in a bscui widget

Usage

set_bscui_selection(widget, selected)
set_bscui_selection(widget, selected)

Arguments

`widget`	a `bscui` object
`selected`	identifiers of pre-selected identifiers

Value

The modified bscui object

Examples

##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}
##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}

Set styles of elements of a bscui widget

Description

Set styles of elements of a bscui widget

Usage

set_bscui_styles(
  widget,
  element_styles,
  to_ignore = NULL,
  targeted_tags = widget$x$structure_shapes,
  append = FALSE
)
set_bscui_styles(
  widget,
  element_styles,
  to_ignore = NULL,
  targeted_tags = widget$x$structure_shapes,
  append = FALSE
)

Arguments

`widget`	a `bscui` object
`element_styles`	NULL or a data frame with an id column providing the element identifier and one column per style name. Column names should correspond to a style name in camel case (e.g., "strokeOpacity").
`to_ignore`	identifiers of elements to ignore: if those elements are children of elements to update they won't be updated
`targeted_tags`	targeted_tags affected tag names (by default: structure_shapes of the scui object)
`append`	if TRUE the value will be concatenate with the existing value

Value

The modified bscui object

Examples

##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}
##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}

Set UI elements of a bscui widget

Description

Set UI elements of a bscui widget

Usage

set_bscui_ui_elements(widget, ui_elements)
set_bscui_ui_elements(widget, ui_elements)

Arguments

a bscui object

ui_elements

NULL or a data frame with the following columns:

id: the element identifier
ui_type: either "selectable" (several elements can be selected), "button" (action will be triggered on click), "none" (no ui)
title: a description of the element to display on mouseover event

Value

The modified bscui object

Examples

##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}
##################################@
### Preparing data ----

library(bscui)
library(xml2)
library(readr)
library(dplyr)

svg <- xml2::read_xml(system.file(
   "examples", "Animal_cells.svg.gz",
   package="bscui"
))
info <- readr::read_tsv(system.file(
   "examples", "uniprot_cellular_locations.txt.gz",
   package="bscui"
), col_types=strrep("c", 6)) |>
   mutate(id = sub("-", "", `Subcellular location ID`))

##################################@
### Building the figure ----

figure <- bscui(svg) |>
   set_bscui_ui_elements(
      info |>
         mutate(
            ui_type = "selectable",
            title = Name
         ) |>
         select(id, ui_type, title)
   ) |>
   set_bscui_styles(
      info |>
         filter(Name == "Cytosol") |>
         mutate(fill = "#FF7F7F") |>
         select(id, fill)
   ) |>
   set_bscui_attributes(
      info |>
         filter(Name == "Cytoskeleton") |>
         mutate(display = "none") |>
         select(id, display)
   ) |>
   set_bscui_selection("SL0188") |>
   set_bscui_options(zoom_min=1, clip=TRUE)
figure

##################################@
### Saving the figure ----

if(interactive()){
   ## Temporary directory to save example file
   tdir <- tempdir()

   ## Interactive html file
   f_path <- file.path(tdir, "figure.html")
   figure |> htmlwidgets::saveWidget(file=f_path)
   cat(f_path)

   ## PNG image
   f_path <- file.path(tdir, "figure.png")
   figure |>
      set_bscui_options(show_menu = FALSE) |>
      export_bscui_to_image(file=f_path, zoom=2)
   cat(f_path)
}

Update the attributes of bscui elements in 'shiny' app

Description

Update the attributes of bscui elements in 'shiny' app

Usage

update_bscui_attributes(
  proxy,
  element_attributes,
  to_ignore = NULL,
  targeted_tags = NULL
)
update_bscui_attributes(
  proxy,
  element_attributes,
  to_ignore = NULL,
  targeted_tags = NULL
)

Arguments

`proxy`	a `bscui_Proxy` object
`element_attributes`	a data frame with an id column providing the element identifier and one column per attribute name.
`to_ignore`	of elements to ignore: if those elements are children of elements to update they won't be updated. This parameter is not taken into account when there is no "id" column in the element_styles data frame.
`targeted_tags`	affected tag names. If NULL (default), the structure_shapes of the `bscui` object

Value

the provided proxy object

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Replace current selection with given element identifiers

Description

Replace current selection with given element identifiers

Usage

update_bscui_selection(proxy, element_ids)
update_bscui_selection(proxy, element_ids)

Arguments

`proxy`	a `bscui_Proxy` object
`element_ids`	element identifiers to add to the selection; empty clear the selection

Value

the provided proxy object

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Update the style of bscui elements in 'shiny' app

Description

Update the style of bscui elements in 'shiny' app

Usage

update_bscui_styles(
  proxy,
  element_styles,
  to_ignore = NULL,
  targeted_tags = NULL,
  append = FALSE
)
update_bscui_styles(
  proxy,
  element_styles,
  to_ignore = NULL,
  targeted_tags = NULL,
  append = FALSE
)

Arguments

`proxy`	a `bscui_Proxy` object
`element_styles`	a data frame with an "id" column and one column per style to apply. If the "id" column is missing, then the modifications apply to the svg selected elements.
`to_ignore`	of elements to ignore: if those elements are children of elements to update they won't be updated. This parameter is not taken into account when there is no "id" column in the element_styles data frame.
`targeted_tags`	affected tag names. If NULL (default), the structure_shapes of the `bscui` object
`append`	if TRUE the value will be concatenate with the existing value

Value

the provided proxy object

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Update the type and title of bscui ui elements in 'shiny' app

Description

Update the type and title of bscui ui elements in 'shiny' app

Usage

update_bscui_ui_elements(proxy, ui_elements)
update_bscui_ui_elements(proxy, ui_elements)

Arguments

proxy

a bscui_Proxy object

ui_elements

NULL or a data frame with the following columns:

id: the element identifier
ui_type: either "selectable" (several elements can be selected), "button" (action will be triggered on click), "none" (no ui)
title: a description of the element to display on mouseover event

Value

the provided proxy object

Examples

if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}
if(interactive()){
   from_shiny <- new.env()
   shiny::runApp(system.file(
      "examples", "shiny-anatomogram", package = "bscui"
   ))
   for(n in names(from_shiny)){
      bscui(from_shiny[[n]]) |> print()
   }
}

Package 'bscui'

Help Index

Add an SVG element to the UI

Description

Usage

Arguments

Value

Examples

Build SVG Custom User Interface

Description

Usage

Arguments

Value

Examples

'shiny' bindings for bscui

Description

Usage

Arguments

Details

Value

See Also

Examples

Manipulate an existing bscui instance in a 'shiny' app

Description

Usage

Arguments

Details

Value

See Also

Examples

Trigger a click event on a clickable element

Description

Usage

Arguments

Value

Examples

Save a bscui widget to an image file

Description

Usage

Arguments

Value

See Also

Examples

Get the displayed SVG

Description

Usage

Arguments

Value

Examples

Change element order in the SVG

Description

Usage

Arguments

Value

Examples

Remove SVG elements from the UI

Description

Usage

Arguments

Value

Examples

Set attributes of elements of a bscui widget

Description

Usage

Arguments

Value

Examples

Set options of bscui widget

Description

Usage

Arguments

Value

Examples

Pre-select UI elements in a bscui widget

Description

Usage

Arguments

Value

Examples

Set styles of elements of a bscui widget