EpivizApp-class: 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
EpivizData 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.
navigate(chr, start, end)- Navigate to given position on the epiviz app.
plot(data_object, 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.
- ...
- 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.
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.