plot_clustSep: scClustViz plot: Cluster separation boxplots

In BaderLab/scClustViz: Differential Expression-based scRNAseq Cluster Assessment and Viewing

scClustViz plot: Cluster separation boxplots

Description

This function plots metrics of cluster solution cohesion or overfitting as a function of the number of clusters found.

Usage

plot_clustSep(sCVdL, DEtype, FDRthresh = 0.05, res, Xlim, Ylim)

Arguments

sCVdL	A named list of sCVdata objects, output of CalcAllSCV.
DEtype	One of "DEneighb", "DEmarker", or "silWidth". "DEneighb" shows number of significantly differentially expressed genes between nearest neighbouring clusters. "DEmarker" shows number of marker genes per cluster, significantly positively differentially expressed genes in all pairwise comparisons with other clusters. "silWidth" shows silhouette widths with average silhouette width as a trace across all clustering solutions. (see silhouette).
FDRthresh	Default=0.05. The false discovery rate threshold for determining significance of differential gene expression.
res	Optional. Name of cluster resolution to highlight. Must be one of names(sCVdL).
Xlim	Optional. Passed to plot.default(xlim=Xlim).
Ylim	Optional. Passed to plot.default(ylim=Ylim).

Examples

## Not run: 
plot_clustSep(sCVdL,DEtype="DEneighb",FDRthresh=0.05,res="res.0.8")

## End(Not run)

BaderLab/scClustViz documentation built on Sept. 10, 2023, 11:51 p.m.