TreeViz: The TreeViz class.

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

Description

SummarizedExperiment-like class for datasets that have hierarchies on either rowData or colData. For microbiome data, rowData is a tree hierarchy For single cell data, colData is a tree hierarchy

Usage

TreeViz(assays = SimpleList(), rowData = NULL, colData = NULL, ...)

Arguments

assays	simple list of counts
rowData	rowData
colData	colData
...	other parameters for SummarizedExperiment

Value

a 'TreeViz' object

Examples

library(metagenomeSeq)
data(mouseData)
counts <- MRcounts(mouseData)
hierarchy <- fData(mouseData)
tree <- TreeIndex(hierarchy)
mbiome <- TreeViz(SimpleList(counts=counts), rowData=tree)

HCBravoLab/palmtree documentation built on Dec. 17, 2021, 10:25 p.m.