EpivizTreeData-class: Data container for MRexperiment objects

In jkanche/TreeSE: R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

Description

Used to serve hierarchical data (used in e.g., icicle plots and heatmaps).

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

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

getReducedDim(method = NULL, gene = NULL)

Compute PCA over all features for given samples

method

which dimension to access

gene

send expression of a gene back with the dimensions

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

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

jkanche/TreeSE documentation built on Oct. 1, 2021, 8:31 p.m.