clusteringDendrogram: Make a clustering dendrogram with coloring by experimental...

In pinin4fjords/shinyngs: Shiny apps for NGS data

Make a clustering dendrogram with coloring by experimental variable

Description

A simple function using ggdendro to make a sample dendrogram

Usage

clusteringDendrogram(
  plotmatrix,
  experiment,
  colorby = NULL,
  cor_method = "pearson",
  cluster_method = "ward.D",
  plot_title = "",
  labelspace = 0.2,
  palette = NULL,
  palette_name = "Set1"
)

Arguments

plotmatrix	Expression/ other data matrix
experiment	Annotation for the columns of plotmatrix
colorby	Column name in experiment specifying how boxes should be colored
cor_method	Correlation method, passed to cor() (default: pearson).
cluster_method	Clustering method, passed to hclust() (default: ward.D).
plot_title	Plot title
labelspace	Vertical fraction of plot to be used for labels (default: 0.2).
palette	Palette of colors, one for each unique value derived from colorby.
palette_name	Valid R color palette name

Value

output A ggplot output

Examples

# Make a dendrogram with the data in airway

require(airway)
data(airway, pakckage = "airway")
clusteringDendrogram(assays(airway)[[1]], data.frame(colData(airway)), colorby = "dex")

# Do the same, but only usig the 1000 most variant rows and see how the
# clustering improves.

mymatrix <- assays(airway)[[1]]
mymatrix <- mymatrix[order(apply(mymatrix, 1, var), decreasing = TRUE)[1:1000], ]
clusteringDendrogram(mymatrix, data.frame(colData(airway)), colorby = "dex")

pinin4fjords/shinyngs documentation built on Feb. 28, 2024, 10:19 a.m.