plot_matrix_dendrogram: Plot a clustered dendrogram

In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description

Draws a clustered heatmap using clustering methods implemented in the popular R package pheatmap. Returns a ggplot2 object

Usage

plot_matrix_dendrogram(matrix, scale = "row", cluster = "col",
  clustering_distance = "euclidean", clustering_method = "complete")

Arguments

matrix	a matrix of values
scale	"rows" or "cols" or "none"; indicates whether values should be centered and scaled in the row direction or the column direction or none.
cluster	"rows" or "cols"; whether to cluster rows or columns.
clustering_distance	distance measure to be used. Possible values are "correlation", "euclidean", "maximum", "manhattan", "canberra", "binary", or "minkowski" (defined in dist() function.)
clustering_method	clustering method to be used. Accepts the same values as hclust: "ward.D", "ward.D2", "single", "complete", "average" (=UPGMA), "mcquitty" (=WPGMA), "median" (=WPGMC) or "centroid" (=UPGMC).

Value

a ggplot2 object

Examples

plot_matrix_heatmap(matrix)

jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.