FindAllmarkers => Doheatmap => Heterogeneous clusters

[karabicicim]

Dear Seurat team,

I would like to ask about my problem with the heatmap plot. After I created a subset for my neutrophil clusters find markers using FindAllmarkers and create heatmap. Surprisingly I observed a heterogenous gene expression patterning inside clusters even when I increased my resolution it still looked the same. How can I fix this? I checked old issues but can not find specific ones. If it is already been asked before can anyone guide me from there?

Thank you!

Specially Cluster 0 has this heterogenous gene expression mostly, but also 2 and 4 have them.

When ı increase res still the same problem.

library(MAST)
Idents(harmony_Neu) <- "SCT_snn_res.1.4"
levels(harmony_Neu)
DefaultAssay(harmony_Neu) <- "RNA"
harmony_Neu <- NormalizeData(harmony_Neu)
#findmarkers
harmony_Neu_1.4<- FindAllMarkers(object = harmony_Neu, only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25, test.use="MAST") %>% dplyr::filter(p_val_adj<0.05)

#top20
harmony_Neu_1.4_top20 <- harmony_Neu_1.4 %>% group_by(cluster) %>% top_n(n = 20, wt = avg_log2FC)
write.csv(harmony_Neu_1.4_top20, file = "harmony_Neu_1.4_top20.csv", row.names = TRUE)

p <-DoHeatmap(harmony_Neu, features = harmony_Neu_1.4_top20$gene)
plot(p)