plot_colored_dendrogram: Plot dendrogram colored by sample definition

In AlexGa/GraftingScripts: Reproducible scripts for studying the graft formation

Description

Does a hierarchical clustering of the data and draws a dendrogam with colored branches and leaved based on the sample definition.

Usage

plot_colored_dendrogram(exp_data,groups, method="pearson", link="average", do.legend=F, unClusteredBranchColor="black", legend.pos = "topright", ...)

Arguments

exp_data	expression matrix, columns represent the samples and rows the genes (or transcripts)
groups	numeric vector describing the relationships of columns to certain groups (like biological replicates)
method	character string defining which correlation coefficient should be used as similarity measure pearson (default), spearman, or kendall
link	character sting defining which agglomeration method to be used. Default: "average". For more information see parameter method at hclust
do.legend	boolean value defining if a color legend should be ploted
unClusteredBranchColor	character string defining the color to use if two brnaches belong to different sample types
legend.pos	character string defining the position of the legend e.g. "topright" (default), "topleft",... legend
...	optional plot parameters plot

Value

a plot

Author(s)

Alexander Gabel

AlexGa/GraftingScripts documentation built on May 26, 2019, 9:34 a.m.