EpivizMetagenomicsData-class: Data container for MRexperiment objects

In metavizr: R Interface to the metaviz web app for interactive metagenomics data analysis and visualization

Description

Used to serve metagenomic data (used in e.g., icicle plots and heatmaps). Wraps MRexperiment-class objects.

Methods

df_to_tree(root, df)

Helper function to recursively build nested response for getHierarchy

root

Root of subtree

df

data.frame containing children to process

get_default_chart_type()

Get name of default chart type for this data type

get_measurements()

Get description of measurements served by this object

getAlphaDiversity(measurements = NULL)

Compute alpha diversity using vegan for the given samples

measurements

Samples to compute alpha diversity

start

Start of feature range to query

end

End of feature range to query

getCombined(measurements = NULL, seqName, start = 1, end = 1000, order = NULL, nodeSelection = NULL, selectedLevels = NULL)

Return the counts aggregated to selected nodes for the given samples

measurements

Samples to get counts for

seqName

name of datasource

start

Start of feature range to query

end

End of feature range to query

order

Ordering of nodes

nodeSelection

Node-id and selectionType pairs

selectedLevels

Current aggregation level

getHierarchy(nodeId = NULL)

Retrieve feature hierarchy information for subtree with specified root

nodeId

Feature identifier with level info

getPCA(measurements = NULL)

Compute PCA over all features for given samples

measurements

Samples to compute PCA over

start

Start of feature range to query

end

End of feature range to query

getRows(measurements = NULL, start = 1, end = 1000, selectedLevels = 3, selections = NULL)

Return the sample annotation and features within the specified range and level for a given sample and features

measurements

Samples to retrieve for

start

Start of feature range to query

end

End of feature range to query

selections

Node-id and selectionType pairs

selectedLevels

Current aggregation level

getValues(measurements = NULL, start = 1, end = 1000, selectedLevels = 3, selections = NULL, row_order = NULL)

Return the counts for a sample within the specified range

measurements

Samples to get counts for

start

Start of feature range to query

end

End of feature range to query

selections

Node-id and selectionType pairs

selectedLevels

Current aggregation level

propagateHierarchyChanges(selection = NULL, order = NULL, selectedLevels = NULL, request_with_labels = FALSE)

Update internal state for hierarchy

selection

Node-id and selectionType pairs

order

Ordering of features

selectedLevels

Current aggregation level

request_with_labels

For handling requests using fData entries from MRexperiment

row_to_dict(row)

Helper function to format each node entry for getHierarchy response

row

Information for current node.

searchTaxonomy(query = NULL, max_results = 15)

Return list of features matching a text-based query

query

String of feature for which to search

max_results

Maximum results to return

toNEO4JDbHTTP(batch_url, neo4juser, neo4jpass, datasource, description = NULL)

Write an 'EpivizMetagenomicsData' object to a Neo4j graph database

@param batch_url (character) Neo4j database url and port for processing batch http requests @param neo4juser (character) Neo4j database user name @param neo4jpass (character) Neo4j database password @param datasource (character) Name of Neo4j datasource node for this 'EpivizMetagenomicsData' object

@examples library(metagenomeSeq) data("mouseData") mobj <- metavizr:::EpivizMetagenomicsData$new(object=mouseData) mobj$toNEO4JDbHTTP(batch_url = "http://localhost:7474/db/data/batch", neo4juser = "neo4juser", neo4jpass = "neo4jpass", datasource = "mouse_data")

update(new_object, send_request = TRUE)

Update underlying data object with new object

Examples

## Not run: 
library(metagenomeSeq)
data(mouseData)
obj <- metavizr:::EpivizMetagenomicsData$new(mouseData, feature_order = colnames(fData(mouseData)))

## End(Not run)

metavizr documentation built on Nov. 8, 2020, 5:13 p.m.