Lineage_plot: Generate genotype plot (scatter plot) for each region and...

In seasoncloud/Alleloscope: Allele-specific copy number genotyping for single cell sequencing data

Generate genotype plot (scatter plot) for each region and save in the plot directory.

Description

Generate genotype plot (scatter plot) for each region and save in the plot directory.

Usage

Lineage_plot(
  Obj_filtered = NULL,
  nSNP = 0,
  clust_method = "ward.D2",
  nclust = 5,
  plot_conf = FALSE,
  plot_path = NULL,
  all_chr = FALSE,
  maxcp = 6
)

Arguments

Obj_filtered	An Alleloscope object with a n cell by (m region * 2) genotype_values matrix and seg_table_filtered matrix. Every 2 columns in the genotype_values matrix are (rho_hat, theta_hat) of each region.
nSNP	An integer for the minimum number of SNPs across segments. Segments with the number of SNPs < nSNP are excluded.
clust_method	Method for clustering. Please refer to the "pheatmap" function.
nclust	An integer for the number of subclones gapped in the plot.
plot_conf	Logical (TRUE/FALSE). Whether or not to plot the confidence scores under the lineage tree.
plot_path	The path for saving the plot.
all_chr	Logical (TRUE/FALSE). Whether or not the analysis is at the whole-genome level.
maxcp	Integer. Setting the maximum number of copies for the analysis.

Value

Plot the lineage tree constructed using cell-level genotypes across all regions and return a vector indicating the cluster identity (of the nclust clusters) of each cell.

seasoncloud/Alleloscope documentation built on March 17, 2023, 1:14 a.m.