Package 'epivizr'

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.

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Class encapsulating a chart in epiviz app

Description

Class encapsulating a chart in epiviz app

Methods

get_app_id(id)

Get chart's id assigned by epiviz app.

get_colors()

Get color palette applied to the chart.

get_id()

Get chart's id assigned by chart manager

get_measurements()

Get measurements for the chart.

get_settings()

Get custom settings for the chart.

get_source_name()

Get chart's id assigned by chart manager

is_connected()

Returns TRUE if chart is connected to a chart on epiviz app.

print_info()

Print settings and color currently used in chart object.

set(settings = NULL, colors = NULL)

Set settings and colors used in chart.

settings

List of settings to apply.

colors

Character vector of HEX colors to use in chart.

set_app_id(id)

Set chart's id assigned by epiviz app.

set_colors(colors)

Set custom colors for the chart.

set_id(id)

Set chart's id assigned by chart manager.

set_settings(settings)

Set custom settings for the chart. Returns subset of valid settings.

settings

List of settings to apply.

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Class providing chart manager for epiviz app

Description

Class providing chart manager for epiviz app

Methods

add_chart(chart_object, send_request = TRUE)

Add a chart to the chart manager.

chart_object

an object of class EpivizChart

send_request

send request to app through websocket

get_chart_colors(chart_object_or_id)

List colors used in a specific chart object.

chart_object_or_id

An object of class EpivizChart or a string indicating the chart's id assigned by chart manager

get_chart_settings(chart_object_or_id)

List chart settings for a specific chart object.

chart_object_or_id

An object of class EpivizChart or a string indicating the chart's id assigned by chart manager

is_server_closed()

Returns TRUE if underlying server is closed. See is_closed method in class EpivizServer.

list_chart_type_colors(chart_type)

List colors currently used in given chart type

list_chart_type_settings(chart_type)

List available settings for a specific chart type.

chart_type

the name for a chart type in R (e.g., 'BlocksTrack', 'StackedLineTrack')

list_chart_types(col_width = 80)

List charts types registered in epivizr with their default settings and colors. Returns a data.frame listing available chart types and a summary of the settings that can be modified.

col_width

Maximum length of settings list displayed.

list_charts()

Return data.frame describing charts loaded by chart manager

num_charts()

Return the number of charts currently loaded through manager.

plot(measurement_object, settings = NULL, colors = NULL, send_request = TRUE)

Visualize data in an EpivizData object using its default chart type. The method get_default_chart_type in class EpivizData is used to determine which chart type is used.

measurement_object

an object of class EpivizData

settings

list of settings to use in chart (uses default chart settings if NULL)

colors

character vector of HEX colors to use in chart (uses default chart colors if NULL)

print_chart(chart_object_or_id, file_name = NULL, file_type = c("pdf", "png"))

Print specific chart to file.

chart_object_or_id

An object of class EpivizChart or a string indicating the chart's id assigned by chart manager.

file_name

Name of file to print to.

file_type

Type of file to print. One of pdf or png.

print_chart_info(chart_object_or_id)

Print settings and colors used in a specific chart object.

chart_object_or_id

An object of class EpivizChart or a string indicating the chart's id assigned by chart manager

print_chart_type_info(chart_type)

Print settings and color information for a given chart type

chart_type

the name for a chart type in R (e.g., 'BlocksTrack', 'StackedLineTrack')

register_chart_type( chart_type, js_chart_type = paste0("epiviz.plugins.charts.", chart_type), js_chart_settings = list(), js_chart_colors = character() )

Register a chart type name to a JavaScript chart type in the epiviz app.

chart_type

the name to use for chart type in R (e.g., 'BlocksTrack')

js_chart_type

the full JavaScript class name of the corresponding chart type (e.g. 'epiviz.plugins.charts.BlocksTrack'). If missing it is taken from the chart_type argument

js_chart_settings

custom settings that can be applied to this chart type in JS.

js_chart_colors

default color palette applied to this chart type in JS.

revisualize(chart_type, chart, ...)

Revisualize uses data the given chart and replots it in the given chart type. The argument chart must be non-NULL.

chart_type

a chart type registered using the register_chart_type method

chart

a chart that includes measurements to be used in a new chart

rm_all_charts()

Remove all charts loaded by chart manager.

rm_chart(chart_object_or_id)

Remove chart from chart manager.

chart_object_or_id

An object of class EpivizChart or a string indicating the chart's id assigned by chart manager

set_chart_settings(chart_object_or_id, settings = NULL, colors = NULL)

Apply custom chart settings or colors to a chart object.

chart_object_or_id

An object of class EpivizChart or a string indicating the chart's id assigned by chart manager

settings

a list of settings to apply to the chart

colors

a list of (HEX code) colors to use in the chart

visualize( chart_type, measurements = NULL, datasource = NULL, settings = NULL, colors = NULL, send_request = TRUE, ... )

Visualize data use the given chart type. One of arguments measurements or datasource must be non-NULL. If measurements is NULL, the get_measurements method in class EpivizData is used to decide which measurements are used in the chart

chart_type

a chart type registered using the register_chart_type method

measurements

a list of EpivizMeasurement objects describing measurements to include in the chart

datasource

an object of class EpivizData, all available measurements from datasource are used as appropriate

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Restart epiviz app connection and workspace.

Description

Restart epiviz app connection and workspace.

Usage

restartEpiviz(file, open_browser = TRUE, host = NULL, envir = parent.frame())

Arguments

file	(character) The name of the file that holds the EpivizApp object to be restarted, ending in .rda.
open_browser	(logical) browse to the epiviz URL before exiting function.
host	(character) name of epiviz app host to open at restart
envir	(environment) environment in which to evaluate expressions needed to reconstruct data sources

Value

An object of class EpivizApp

Examples

# see package vignette for example usage
app <- startEpiviz(non_interactive=TRUE, open_browser=TRUE)
file_name <- tempfile(fileext=".rda")
app$save(file=file_name)
app$stop_app()

app <- restartEpiviz(file=file_name, open_browser=FALSE)

---

Print information about EpivizChart

Description

Print information about EpivizChart

Usage

## S4 method for signature 'EpivizChart'
show(object)

Arguments

object

an EpivizChart object

Value

Nothing, this function is called for its side-effects

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Start epiviz app and create EpivizApp object to manage connection.

Description

Start epiviz app and create EpivizApp object to manage connection.

Usage

startEpiviz(
  host = NULL,
  http_port = NULL,
  path = NULL,
  use_devel = FALSE,
  chr = "chr11",
  start = 99800000,
  end = 103383180,
  debug = FALSE,
  workspace = NULL,
  scripts = NULL,
  gists = NULL,
  use_cookie = TRUE,
  register_function = .register_all_the_epiviz_things,
  open_browser = TRUE,
  server = NULL,
  browser_fun = utils::browseURL,
  ws_host = "localhost",
  ...
)

Arguments

host	(character) use a host for the epiviz app other than the cbcb.umd.edu hosts.
http_port	(integer) port at host serving the epiviz app.
path	(character) path at host where epiviz app is located.
use_devel	(logical) use the devel epiviz application server (http://epiviz-dev.cbcb.umd.edu).
chr	(character) chromosome to browse to on app startup.
start	(integer) start location to browse to on app startup.
end	(integer) end location to browse to on app startup.
debug	(logical) start epiviz app in debug mode.
workspace	(character) a workspace id to load in the epiviz app on startup.
scripts	(character) URLs for JavaScript plugin scripts to be imported when epiviz is loaded (see http://epiviz.cbcb.umd.edu/help for details).
gists	(character) Ids for github gists (http://gist.github.com) containing JavaScript plugin scripts to be imported when epiviz is loaded (see http://epiviz.cbcb.umd.edu/help for details).
use_cookie	(logical) use cookies within the epiviz app.
register_function	(function) function used to register actions and charts on the epiviz app.
open_browser	(logical) browse to the epiviz URL before exiting function.
server	(EpivizServer) if not NULL use this object as underlying WebSocket and HTTP server
browser_fun	(function) function used to browse to URL (browseURL by default)
ws_host	(character) host address to use for websocket connection ("localhost" by default)
...	additional parameters passed to createServer.

Value

An object of class EpivizApp

Examples

# see package vignete for example usage
app <- startEpiviz(non_interactive=TRUE, open_browser=TRUE)
app$stop_app()

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Example methylation data (blocks) for epivizr vignette.

Description

Example results from methylation analysis of human chromosome 11 using the minfi::minfi-package package of TCGA 450k beadarray samples. This object contains large regions of methylation difference between tumor and normal samples obtained from minfi::blockFinder().

Usage

data(tcga_colon_blocks)

Format

A GRanges object with 129 and mcols:

value

average smooth methylation difference within block

area

block area estimate (abs(value) * length)

cluster

id of cluster blockgroup within which block occurs

indexStart

index of first cluster in block

indexEnd

index of last cluster in block

L

number of clusters in block

clusterL

number of probes in block

p.value

permutation p.value based on difference conditioned on length

fwer

family-wise error rate estimate based on difference conditioned on length

p.valueArea

permutation p.value based on area

fwerArea

family-wise error rate estimate based on area

Source

TCGA project: https://tcga-data.nci.nih.gov/tcga/

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Example methylation data (smoothed methylation levels) for epivizr vignette

Description

Example results from methylation analysis of human chromosome 11 using the minfi::minfi-package package of TCGA 450k beadarray samples. This object contains probe cluster level methylation estimates from minfi::blockFinder().

Usage

data(tcga_colon_curves)

Format

A GRanges object with 7135 ranges and mcols:

id

probe cluster id

type

probe cluster type

blockgroup

probe cluster block group

diff

raw methylation percentage difference between normal and tumor

smooth

smooth methylation percentage difference between normal and tumor

normalMean

mean methylation estimate for normal samples

cancerMean

mean methylation estimate for cancer samples

Source

TCGA project: https://tcga-data.nci.nih.gov/tcga/

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Example exon-level RNAseq data from TCGA project for epivizr vignette.

Description

A SummarizedExperiment::RangedSummarizedExperiment object containing exon-level counts from RNAseq data for colon tumor and normal tissue from the TCGA project. Only exons in human chromosome 11 are included.

Usage

data(tcga_colon_expression)

Format

A SummarizedExperiment::RangedSummarizedExperiment object with 12,800 rows (exons) and 40 samples.

assay(tcga_colon_expression)

exon-level count matrix

colData(tcga_colon_expression)

a DataFrame containing sample information. Normal/Tumor status is given in column sample_type

Value

A SummarizedExperiment::RangedSummarizedExperiment object.

Source

TCGA project: https://tcga-data.nci.nih.gov/tcga/

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