EpivizApp-class {epivizr} | R Documentation

## Class managing connection to epiviz application.

### Description

Class managing connection to epiviz application.

### Fields

`server`

  An object of class `EpivizServer` used to communicate with epiviz app.

`data_mgr`

  An object of class `EpivizDataMgr` used to serve data to epiviz app.

`chart_mgr`

  An object of class `EpivizChartMgr` used to manage charts added to epiviz app session.

### Methods

`get_current_location(callback)`

  Obtain current genome location on epiviz app and evaluate callback function on result.

  callback

    A callback function to evaluate on response data. Response data will be a list with slots `seqName`, `start` and `end`

`get_ms_object(chart_id_or_object, index = 1)`

  Get object of class `EpivizData` used as a data source in a given chart.

  chart_id_or_object

    An object of class `EpivizChart` or an id for a chart loaded to the epiviz app.

  index

    Index into `.measurements`

  list of chart object to obtain data object for.

`is_server_closed()`

  Check if underlying server connection is closed.

`load_remote_measurements()`

  Load remote measurements into R session.

`load_workspace(workspace_id = NULL)`

  load an epiviz workspace.

  workspace_id

    Workspace id to load from the database.

`navigate(chr, start, end)`

  Navigate to given position on the epiviz app.

`plot( data_object, datasource_name = NULL, send_request = TRUE, settings = NULL, colors = NULL, ... )`

  Visualize data on epiviz app using its default chart type. Measurements from the `data-object` are first added to the epiviz app using the `add_measurements` method for class `EpivizData`. See documentation for `register` for information on supported data types and the `EpivizData` class encapsulating this type of data. Once measurements are loaded, the `plot` method of class `EpivizChartMgr` is used to plot the data, using the default chart type for this type of data.

  data_object

    An object to plot in epiviz app.

  datasource_name

    Name to use for datasource, parses `data_object` if missing or NULL

  ...

    Additional arguments passed to `add_measurements` method for class `EpivizData`

`print_workspace(file_name = NULL, file_type = "pdf")`

  Save epiviz workspace as a pdf or png.

`save(file, include_data = TRUE)`

  Save EpivizApp object representation of a workspace into .RData file.

  file

    (character) The name of the file to save the EpivizApp object into, ending in .rda.

  stop_app

    (logical) Stop the EpivizApp session.

  include_data

    (logical) Include EpivizApp's data when saving the EpivizApp object.

`service(verbose = TRUE)`

  Block interactive R session to service websocket requests.

`slideshow(granges, n = length(granges), .callback = NULL)`

  Navigate on epiviz app successively to given positions.

  granges

    An object of class `GenomicRanges` indicating set of genomic regions to navigate in epiviz app.

  n

    (integer) The number of regions in `granges` to navigate to.

  .callback

    (function) function to call after navigating to each region. Used for testing purposes.

`stop_app()`

  stop and clean connection to epiviz app.

[Package epivizr version 2.24.0 Index]