plot_psbulk: Plot a pseudobulk HMM profile

In whtns/numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

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 = FALSE,
  exclude_gap = TRUE,
  genome = "hg38",
  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'
raster	logical Whether to raster images

Value

ggplot Plot of pseudobulk HMM profile

Examples

p = plot_psbulk(bulk_example)

whtns/numbat documentation built on Nov. 8, 2022, 10:48 a.m.