plot_psbulk {numbat}

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

Value

ggplot Plot of pseudobulk HMM profile

Examples

p = plot_psbulk(bulk_example)