Genotype: Genotype each cell for each region and plot the genotypes.

Description Usage Arguments Value

View source: R/Genotype.R

Description

Genotype each cell for each region and plot the genotypes.

Usage

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Genotype(
  Obj_filtered = NULL,
  xmax = NULL,
  plot_path = NULL,
  rds_path = NULL,
  ref_gt = NULL,
  cell_type = NULL,
  legend = FALSE
)

Arguments

Obj_filtered

An Alleloscope object with a n cell by (m region * 4) genotype_values matrix. Every 2 columns in the genotype_table matrix are (rho_hat, theta_hat) of each region.

xmax

An integer for the x-axis maximum limit.

plot_path

The path for saving the plot.

rds_path

The path for saving the rds object.

ref_gt

A reference "genotypes" (from scDNA-seq) to help with genotype estimation.

cell_type

A matrix with two columns: COL1- cell barcodes; COL2- cell types ("tumor" and others)

legend

Logical (TRUE/FALSE) Whether or not to show the figure legends.

Value

A list of ggplot objects of the genotyping results for all the regions.


seasoncloud/Alleloscope documentation built on June 18, 2021, 7:24 p.m.