plot_psbulk: Plot a pseudobulk HMM profile
In numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

plot_psbulk

R Documentation

Plot a pseudobulk HMM profile

Description

Plot a pseudobulk HMM profile

Usage

plot_psbulk(
  bulk,
  use_pos = TRUE,
  allele_only = FALSE,
  min_LLR = 5,
  min_depth = 8,
  exp_limit = 2,
  phi_mle = TRUE,
  theta_roll = FALSE,
  dot_size = 0.8,
  dot_alpha = 0.5,
  legend = TRUE,
  exclude_gap = TRUE,
  genome = "hg38",
  text_size = 10,
  raster = FALSE
)

Arguments

`bulk`	dataframe Pseudobulk profile
`use_pos`	logical Use marker position instead of index as x coordinate
`allele_only`	logical Only plot alleles
`min_LLR`	numeric LLR threshold for event filtering
`min_depth`	numeric Minimum coverage depth for a SNP to be plotted
`exp_limit`	numeric Expression logFC axis limit
`phi_mle`	logical Whether to plot estimates of segmental expression fold change
`theta_roll`	logical Whether to plot rolling estimates of allele imbalance
`dot_size`	numeric Size of marker dots
`dot_alpha`	numeric Transparency of the marker dots
`legend`	logical Whether to show legend
`exclude_gap`	logical Whether to mark gap regions and centromeres
`genome`	character Genome build, either 'hg38' or 'hg19'
`text_size`	numeric Size of text in the plot
`raster`	logical Whether to raster images