PlotChrCluster: PlotChrCluster

In bioinformatic-seragnoli/BOBaFIT: Refitting diploid region profiles using a clustering procedure

PlotChrCluster

Description

The function clusters chromosomes based on the copy number (CN) and returns a graph where it is possible to observe the different groups and two data frames (report and plot_table). See the vignette for the data frame descriptions.

Usage

PlotChrCluster(
  segs,
  clust_method = "ward.D2",
  plot_output = TRUE,
  plot_viewer = TRUE,
  plot_save = FALSE,
  plot_format = "png",
  plot_path,
  verbose = FALSE
)

Arguments

segs	data.frame with segments of samples. It must be formatted with correct column names (start, end, ID)
clust_method	clustering method. Default is "ward.D2"
plot_output	Whether to plot refitted profiles (logical)
plot_viewer	Logical parameter. When it is TRUE, the function print the output plot in the R viewer.By default is TRUE.
plot_save	Logical parameter. When it is TRUE, the function save the plot in the chosen path and format. By default is TRUE.
plot_format	File format for the output plots (accepts "png", "jpg", "pdf", "tiff"). By default is "png"
plot_path	Path to save output plots.
verbose	print information about the processes of the function. By default is FALSE

Value

Plot with chromosomes clustered

Examples

data(TCGA_BRCA_CN_segments)
Cluster <- PlotChrCluster(segs=TCGA_BRCA_CN_segments, 
                         clust_method= "ward.D2", 
                         plot_output=FALSE)

bioinformatic-seragnoli/BOBaFIT documentation built on Jan. 29, 2024, 10:27 a.m.