cut_dendro: Cutting dendrograms

In jianhaizhang/spatialHeatmap: spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Cutting dendrograms

Description

This function is designed to cut dendrograms from heirarchical clustering at a certain height and returns the cluster containing the query biomolecule.

Usage

cut_dendro(dendro, h, target)

Arguments

dendro	A dendrogram from heirarchical clustering.
h	A numeric of height for cutting the dendrogram.
target	The target biomoleclue.

Value

A vector of the cluster containing the query biomolecule.

Author(s)

Jianhai Zhang [e-mail]
Dr. Thomas Girke [e-mail]

References

Tal Galili (2015). dendextend: an R package for visualizing, adjusting, and comparing trees of hierarchical clustering. Bioinformatics. DOI: 10.1093/bioinformatics/btv428

Examples

blk.mus.pa <- system.file("extdata/shinyApp/data", "bulk_mouse_cocluster.rds", package="spatialHeatmap") 
blk.mus <- readRDS(blk.mus.pa)
res.hc <- matrix_hm(ID=c('Actr3b'), data=blk.mus, angleCol=60, angleRow=60, cexRow=0.8, cexCol=0.8, 
margin=c(10, 6), static=TRUE, arg.lis1=list(offsetRow=0.01, offsetCol=0.01))
cut_dendro(res.hc$rowDendrogram, h=1000, 'Actr3b')

jianhaizhang/spatialHeatmap documentation built on Nov. 28, 2024, 4:44 p.m.