plot_clusterGenes_markers: 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 marker genes

Description

This function makes a scatterplot of gene detection rate vs. mean detected gene abundance, highlighting genes identified as cell type specific markers by the user. This function will not work unless addCellMarkersToCGS has been run on the sCVdata object prior.

Usage

plot_clusterGenes_markers(sCVd, selClust, cellMarkers)

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.
cellMarkers	The cellMarkers argument from runShiny. A list of marker genes for expected cell types.

Examples

## Not run: 
cellMarkers <- list("Cortical precursors"=c("Mki67","Sox2","Pax6",
                                                  "Pcna","Nes","Cux1","Cux2"),
                          "Interneurons"=c("Gad1","Gad2","Npy","Sst","Lhx6",
                                           "Tubb3","Rbfox3","Dcx"),
                          "Cajal-Retzius neurons"="Reln",
                          "Intermediate progenitors"="Eomes",
                          "Projection neurons"=c("Tbr1","Satb2","Fezf2",
                                                 "Bcl11b","Tle4","Nes",
                                                 "Cux1","Cux2","Tubb3",
                                                 "Rbfox3","Dcx")
                          )
sCVdata <- labelCellTypes(sCVdata,
                          cellMarkers=cellMarkers,
                          symbolMap=NULL)

pdf("filepath.pdf",width=12,height=7)
plot_clusterGenes_markers(sCVd=sCVdata,
                          selClust="1",
                          cellMarkers=cellMarkers)
dev.off()

## End(Not run)

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