Class managing connection to epiviz application.
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.
get_current_location(callback)
Obtain current genome location on epiviz app and evaluate callback function on result.
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.
An object of class EpivizChart
or an id for
a chart loaded to the epiviz app.
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 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.
An object to plot in epiviz app.
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.
(character) The name of the file to save the EpivizApp object into, ending in .rda.
(logical) Stop the EpivizApp session.
(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.
An object of class GenomicRanges
indicating
set of genomic regions to navigate in epiviz app.
(integer) The number of regions in granges
to navigate to.
(function) function to call after navigating to each region. Used for testing purposes.
stop_app()
stop and clean connection to epiviz app.
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