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