plotHMM: Plot zygosity HMM

In quevedor2/WadingPool: A toolkit for shallow/low-pass whole genome sequencing analysis

Description

a 3-4 track visualization of an HMM fitted to a series of observed heterozygous counts. The top track will be a simple count of heterozygous counts along the genome. The middle track(s) will be the estimated state based on a fitted HMM model. If the actual state is known, it will also include the visualization for the actual state on top of the estimated states. The bottom track contains line graphs for the posterior probability of each state.

Usage

plotHMM(model, est_cols, act_cols = NULL, xval = "bin")

Arguments

model	Data frame output fitHmm() function with obs, states, and PP
est_cols	2 element character vector for the estimated [state, state.label] columns
act_cols	If known, 2 element character vector for the actual [state, state.label] columns
xval	String for column ID corresponding to x-axis value (e.g. bin)

Value

a grid object for visualization

quevedor2/WadingPool documentation built on Dec. 22, 2021, 10:59 a.m.