EpivizApp-class: Class managing connection to epiviz application.

Description Fields Methods

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.


epiviz/epivizr documentation built on Oct. 8, 2017, 1:52 p.m.