M3D_Get_Heatmap_Cell_Clusters: Extracts clusters/ordered names from heatmap output

Description Usage Arguments Details Value Examples

Description

Extracts the groupings correponding to the given number of clusters from heatmap output.

Usage

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M3DropGetHeatmapClusters(heatout, k, type="cell")
	M3DropGetHeatmapNames(heatout, type="cell")

Arguments

heatout

Output from a gene-expression heatmap.

k

Number of clusters.

type

One of "cell" or "gene" indicating whether to get clusters or names of cells(columns) or genes(rows).

Details

M3DropGetHeatmapClusters : Traverses down the row or column dendrogram and cuts at the first point where there are at least k clusters. M3DropGetHeatmapNames: gets the names of the cells/genes in the order that they appear on the dendrogram.

Value

A vector of cluster labels for each cell.

Examples

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  library(M3DExampleData)
  genes <- rownames(Mmus_example_list$data)[1:20]
  heatmap_out <- M3DropExpressionHeatmap(genes, Mmus_example_list$data)
  clusters <- M3DropGetHeatmapClusters(heatmap_out, k=5)
  heatmap_gene_labels <- M3DropGetHeatmapNames(heatmap_out, type="gene")

tallulandrews/M3D documentation built on May 31, 2019, 2:55 a.m.