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

Description Usage Arguments Value

View source: R/Lineage_plot.R

Description

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

Usage

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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 Feb. 21, 2022, 9:57 a.m.