Liger find a sub cluster under one cluster

Question

[Andy]

Good morning,

I am trying to use liger to find my sub clusters for one cell clusters. However, I got trouble.

I noticed that my sub clusters looks like:

They are not really clustering.

I am trying to use different parameters, but I found this one looks the best.

My code is:

recluster_data <- FindVariableFeatures(recluster_data) recluster_data <- ScaleData(recluster_data, do.center=FALSE) nFactors=30 #bigger nfactor recluster_data$clusters <- factor(recluster_data$clusters, levels=1:length(levels(recluster_data$clusters)))

聚类

recluster_data <- FindNeighbors(recluster_data, reduction="iNMF", dims=1:nFactors) %>% FindClusters(resolution = 0.2)#resolution recluster_data <- RunUMAP(recluster_data, dims=1:nFactors, reduction="iNMF")

pdf("fibroblastsubclusters.pdf", width = 10, height = 10) DimPlot(recluster_data, reduction = "umap",label = TRUE, pt.size = 3,label.size = 7)

scale_fill_manual(values =c(‘#4575B4’))

dev.off()

[Andy]

The problem can be solved by giving a large value to the 'k' variable and using a large factor number.