plotRegNB: Function for plotting negative binomial regression

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Function for plotting negative binomial regression

Description

This function plots the parameters obatined by the negative binomial regression of the transcript counts on the total transcript count in each cells. Smoothed parameter estimates are also shown.

Usage

plotRegNB(expData, y, par.nb = NULL, span = 0.75, ...)

Arguments

expData	Matrix of gene expression values with genes as rows and cells as columns. The matrix needs to contain the same cell IDs as columns like the input matrix. used to derive the pruned k nearest neighbours with the pruneKnn function.
y	List object returned by the compNoise or pruneKnn function (if run with regNB=TRUE).
par.nb	Parameter to be plotted, i.e. valid column of res$regData$nbRegr. of the log total UMI count. intercept is the intercept inferred by the regression. Default is NULL and theta is shown.
span	Positive real number. Parameter for loess-regression (see large) controlling the degree of smoothing. Default is 0.75.
...	Additional arguments for plot.

Value

None

Examples

res <- pruneKnn(intestinalDataSmall,no_cores=1)
plotRegNB(intestinalDataSmall,res,"theta")

RaceID documentation built on April 4, 2025, 4:34 a.m.