xVServer: Shiny module server for cross-view of multidimensional data

In avucoh/DIVE: Data Integration and Visual Exploration

Shiny module server for cross-view of multidimensional data

Description

Integratively visualize a high-dimensional expression dataset with phenotype or clinical features through clustering, cross-selection and cross-comparison

Usage

xVServer(
  id,
  hdata,
  cdata = reactive(NULL),
  key = "ID",
  selected = reactive(NULL),
  height = 500,
  returndata = NULL
)

Arguments

id	Character ID for specifying namespace, see shiny::NS.
hdata	A numeric matrix with row and column names for heatmap representation.
cdata	Optional, a data.table of characteristics data. See details.
key	Name of key column for cdata, currently defaults to "ID".
selected	A reactive vector used to subset the features (cols) of hdata.
height	Height for data plots.
returndata	A reactive object that can be used to return the local version of data in this module.

Details

The module is geared towards bioinformatics uses; the data objects here can be compared to Biobase::ExpressionSet class object where hdata corresponds to a (transposed) exprs matrix in the assayData slot and cdata corresponds to the data in the phenoData slot.

The capabilities implemented are clustering (of samples by features only) and data subsetting. The data subsetting of expression data works through a "local" selection, which is simply created from column names of the hdata data matrix, or through an alternative/global selection, which is whatever is passed into selected. For alternative/global selection to work, the data must have an alternative index; see xVExprs. Local selection takes precedences over alternative/global selection.

avucoh/DIVE documentation built on Aug. 29, 2023, 6:02 p.m.