plot_sample_tree: Sample clustering

In csbl-usp/CEMiTool: Co-expression Modules identification Tool

Sample clustering

Description

Creates a dendrogram showing the similarities between samples in the expression data.

Usage

plot_sample_tree(cem, ...)

## S4 method for signature 'CEMiTool'
plot_sample_tree(
  cem,
  col_vector = NULL,
  sample_name_column = NULL,
  class_column = NULL,
  filter = FALSE
)

Arguments

cem	Object of class CEMiTool or data.frame.
...	Optional parameters.
col_vector	A vector of columns to use for visualizing the clustering. See Details.
sample_name_column	A string specifying the column to be used as sample identification. For CEMiTool objects, this will be the string specified in the sample_name_column slot.
class_column	A string specifying the column to be used as sample group identification. For CEMiTool objects, this will be the string specified in the class_column slot.
filter	Logical. Whether or not to use filtered data for CEMiTool objects (Default: FALSE).

Value

Object of class CEMiTool with dendrogram or a plot object.

Examples

# Get example CEMiTool object
data(cem)
# Plot sample dendrogram
cem <- plot_sample_tree(cem)
# Check resulting plot
show_plot(cem, "sample_tree")

csbl-usp/CEMiTool documentation built on March 27, 2024, 5:14 a.m.