NCviz-class: Biological profilin data visualisation

In sysbio-curie/cBioFetchR: Extract data from cBioPortal in a way that they can easily be exported to NaviCell

Description

S4 class for biological profiling data visualisation. Contains statistics and functions to communicate with a NaviCell API.

Constructor for the class NCviz. NCviz objects provide functions to visualize profiling data on a NaviCell map

Usage

NCviz(nc_url = "", cell_type = "", annotations = list(),
  cbio_gene_data = list(), cbio_profile_data = list(), nc_data = list(),
  verbose = TRUE)

Arguments

nc_url	URL of the NaviCell server
cell_type	Name of the dataset to pass to the NaviCell server
annotations	Cases annotations (clinical data)
nc_data	Data under the NaviCell format, a list indexed by experiment type containing data arranged in a dataframe with genes HUGO indentifiers as rownames and samples id as colnames (incompatible with cbio_data)
cbio_data	Data loaded with cBioStudy (incompatible with nc_data)

Author(s)

Mathurin Dorel [e-mail]

See Also

cBioStudy

sysbio-curie/cBioFetchR documentation built on May 31, 2019, 12:48 a.m.