plot_clusterGenes_DEgenes: scClustViz plot: Plot within-cluster gene expression...

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

scClustViz plot: Plot within-cluster gene expression highlighting DE genes

Description

This function makes a scatterplot of gene detection rate vs. mean detected gene abundance, highlighting differentially expressed genes.

Usage

plot_clusterGenes_DEgenes(sCVd, selClust, DEgenes, DEnum, DEtype)

Arguments

sCVd	The sCVdata object.
selClust	A named character vector representing the cluster to be displayed. If labelCellTypes has been run, pass the appropriate element of attr(Clusters(sCV),"ClusterNames") to this argument to show both cluster number and cell type label in the legend.
DEgenes	The output of dotplotDEgenes.
DEnum	Single integer representing the maximum number of DE genes per cluster to include in the plot.
DEtype	One of: "DEvsRest" - see DEvsRest; "DEneighb" - see DEneighb; "DEmarker" - see DEmarker.

Examples

## Not run: 
pdf("filepath.pdf",width=12,height=7)
plot_clusterGenes_DEgenes(sCVd=sCVdata,
                          selClust="1",
                          DEgenes=dotplotDEgenes(sCVdata,
                                                 DEtype="DEneighb",
                                                 FDRthresh=0.01),
                          DEnum=5,
                          DEtype="DEneighb")
dev.off()

## End(Not run)

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